From a81f7d5cd3f172ab4e9ce1554a4778f16f98fb48 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Mon, 23 May 2016 10:24:45 +0200 Subject: [PATCH 01/12] Test and update fastx tools --- .tt_blacklist | 16 ---------------- 1 file changed, 16 deletions(-) diff --git a/.tt_blacklist b/.tt_blacklist index d7902283..e100ea5c 100644 --- a/.tt_blacklist +++ b/.tt_blacklist @@ -129,22 +129,6 @@ tool_collections/vcftools/vcftools_merge tool_collections/vcftools/vcftools_subset tool_collections/vcftools/vcftools_annotate tool_collections/vcftools/vcftools_isec -tool_collections/fastx_toolkit/fastq_quality_converter -tool_collections/fastx_toolkit/fasta_clipping_histogram -tool_collections/fastx_toolkit/fastx_nucleotides_distribution -tool_collections/fastx_toolkit/fastx_trimmer -tool_collections/fastx_toolkit/fastx_clipper -tool_collections/fastx_toolkit/fastx_artifacts_filter -tool_collections/fastx_toolkit/fastx_barcode_splitter -tool_collections/fastx_toolkit/fastq_quality_filter -tool_collections/fastx_toolkit/fastx_renamer -tool_collections/fastx_toolkit/fastx_quality_statistics -tool_collections/fastx_toolkit/fasta_formatter -tool_collections/fastx_toolkit/fastq_quality_boxplot -tool_collections/fastx_toolkit/fasta_nucleotide_changer -tool_collections/fastx_toolkit/fastq_to_fasta -tool_collections/fastx_toolkit/fastx_collapser -tool_collections/fastx_toolkit/fastx_reverse_complement tool_collections/gatk/variant_annotator tool_collections/gatk/variant_apply_recalibration tool_collections/gatk/count_covariates From a5543135b8de909d6639807bc48b2dd503833a8f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Mon, 23 May 2016 10:26:53 +0200 Subject: [PATCH 02/12] Upgrade to newer version of fastx Unfortunately tests are missing --- .../fasta_clipping_histogram.xml | 12 +++++++----- .../fasta_formatter/fasta_formatter.xml | 4 ++-- .../fasta_formatter/tool_dependencies.xml | 4 ++-- 3 files changed, 11 insertions(+), 9 deletions(-) diff --git a/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml b/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml index 7275e20e..8873a2ea 100644 --- a/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml +++ b/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml @@ -1,14 +1,16 @@ - + chart - fastx_toolkit + fastx_toolkit - fasta_clipping_histogram.pl $input $outfile - + + fasta_clipping_histogram.pl + '$input' + '$outfile' + - diff --git a/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml b/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml index 52a53ce4..bc622c37 100644 --- a/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml +++ b/tool_collections/fastx_toolkit/fasta_formatter/fasta_formatter.xml @@ -1,7 +1,7 @@ - + formatter - fastx_toolkit + fastx_toolkit - + diff --git a/tool_collections/fastx_toolkit/fasta_formatter/fastx_macros.xml b/tool_collections/fastx_toolkit/fasta_formatter/fastx_macros.xml new file mode 120000 index 00000000..a6c33dbb --- /dev/null +++ b/tool_collections/fastx_toolkit/fasta_formatter/fastx_macros.xml @@ -0,0 +1 @@ +../fastx_macros.xml \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fasta_formatter/tool_dependencies.xml b/tool_collections/fastx_toolkit/fasta_formatter/tool_dependencies.xml deleted file mode 100644 index 708bedeb..00000000 --- a/tool_collections/fastx_toolkit/fasta_formatter/tool_dependencies.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - - - diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml index e15c6060..9f94eb60 100644 --- a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml +++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml @@ -1,8 +1,9 @@ - + converter - - fastx_toolkit - + + + fastx_macros.xml + + - - fastx_toolkit - - fastq_quality_boxplot_graph.sh -t '$input.name' -i $input -o $output - + + + fastx_macros.xml + + + fastq_quality_boxplot_graph.sh -t '$input.name' -i '$input' -o '$output' + @@ -12,6 +14,12 @@ + + + + + + **What it does** diff --git a/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastx_macros.xml b/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastx_macros.xml new file mode 120000 index 00000000..a6c33dbb --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_quality_boxplot/fastx_macros.xml @@ -0,0 +1 @@ +../fastx_macros.xml \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastq_quality_boxplot/test-data/fastq_stats1.out b/tool_collections/fastx_toolkit/fastq_quality_boxplot/test-data/fastq_stats1.out new file mode 100644 index 00000000..852c8122 --- /dev/null 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z#@l;S?$6+90Je!6HfMBg%i62`Uh=^G*Z=pf`W<~ywQ1GrPyMyCHvMn^*Z;43-M;C0 zD}Mj=JNxO_@3~WC#2Ng64aPaHkKfme+E3tN_y6Dip`XmK!!~c-@xQZP6?y|l zW}ZuPf)_hBY<|JL6*y+N=k>ldt7c~(10Ga$pyKlv*TCslZ&dLxe2%;Pm&pP+%26QZ zyj8BG{bOw4ue3Gy&nC_P_A(xLV%0xY2Aj983=lhy)&S4TTV&ny9=Olv&JWk`*MWm@ z%Ru&2g8cD4^`Fzr8J7KKEieO4b?dY_-JQ$6!2Vaf`MPz- z_`jY9?v4Mu{NL{Wf4uTv_rJehe`UYD=!XiRWo|&z - - - - - diff --git a/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml b/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml index c143cb89..e8c23208 100644 --- a/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml +++ b/tool_collections/fastx_toolkit/fastq_quality_converter/fastq_quality_converter.xml @@ -1,8 +1,9 @@ - + (ASCII-Numeric) - - fastx_toolkit - + + + fastx_macros.xml + - - - - - diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml b/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml index ba360c7f..8552b5d4 100644 --- a/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml +++ b/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml @@ -1,8 +1,9 @@ - + - - fastx_toolkit - + + + fastx_macros.xml + - - - - - diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml index 410aa022..82cdfa31 100644 --- a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml @@ -1,12 +1,13 @@ - + converter from FASTX-toolkit - - fastx_toolkit - + + + fastx_macros.xml + gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v -#if $input.ext == "fastqsanger": --Q 33 -#end if + #if $input.ext == "fastqsanger": + -Q 33 + #end if diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/fastx_macros.xml b/tool_collections/fastx_toolkit/fastq_to_fasta/fastx_macros.xml new file mode 120000 index 00000000..a6c33dbb --- /dev/null +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/fastx_macros.xml @@ -0,0 +1 @@ +../fastx_macros.xml \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastq_to_fasta/tool_dependencies.xml deleted file mode 100644 index 5474ad78..00000000 --- a/tool_collections/fastx_toolkit/fastq_to_fasta/tool_dependencies.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - - - diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml b/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml index 4f7505f5..b7d55cc9 100644 --- a/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml +++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml @@ -1,8 +1,9 @@ - + - - fastx_toolkit - + + + fastx_macros.xml + - - - - - diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml index 3f627f3d..39c009f2 100644 --- a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml @@ -1,9 +1,11 @@ - + - - fastx_toolkit - - fastx_barcode_splitter_galaxy_wrapper.sh '$BARCODE' '$input' "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > '$output' + + + fastx_macros.xml + + + '$__tool_directory__'/fastx_barcode_splitter_galaxy_wrapper.sh '$BARCODE' '$input' "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > '$output' diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_macros.xml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_macros.xml new file mode 120000 index 00000000..a6c33dbb --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_macros.xml @@ -0,0 +1 @@ +../fastx_macros.xml \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/tool_dependencies.xml deleted file mode 100644 index 5474ad78..00000000 --- a/tool_collections/fastx_toolkit/fastx_barcode_splitter/tool_dependencies.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - - - diff --git a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml index 2fb04f55..493cc0fa 100644 --- a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml +++ b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml @@ -1,8 +1,9 @@ - + adapter sequences - - fastx_toolkit - + + + fastx_macros.xml + - - - - - diff --git a/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml index 1f5e0a25..7e2b1015 100644 --- a/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml +++ b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml @@ -1,15 +1,16 @@ - + sequences - - fastx_toolkit - + + + fastx_macros.xml + - + diff --git a/tool_collections/fastx_toolkit/fastx_collapser/fastx_macros.xml b/tool_collections/fastx_toolkit/fastx_collapser/fastx_macros.xml new file mode 120000 index 00000000..a6c33dbb --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_collapser/fastx_macros.xml @@ -0,0 +1 @@ +../fastx_macros.xml \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastx_collapser/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_collapser/tool_dependencies.xml deleted file mode 100644 index 5474ad78..00000000 --- a/tool_collections/fastx_toolkit/fastx_collapser/tool_dependencies.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - - - diff --git a/tool_collections/fastx_toolkit/fastx_macros.xml b/tool_collections/fastx_toolkit/fastx_macros.xml new file mode 100644 index 00000000..bca9a9cf --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_macros.xml @@ -0,0 +1,10 @@ + + 1.14 + + + + fastx_toolkit + + + + \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_macros.xml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_macros.xml new file mode 120000 index 00000000..a6c33dbb --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_macros.xml @@ -0,0 +1 @@ +../fastx_macros.xml \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml index 7bb498e9..0d1abd22 100644 --- a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml +++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml @@ -1,17 +1,24 @@ - + - - fastx_toolkit - + + gnuplot + + + fastx_macros.xml + fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output - - + + + + + + **What it does** diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/test-data/fastq_stats1.out b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/test-data/fastq_stats1.out new file mode 100644 index 00000000..852c8122 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/test-data/fastq_stats1.out @@ -0,0 +1,37 @@ +column count min max sum mean Q1 med Q3 IQR lW rW A_Count C_Count G_Count T_Count N_Count Max_count +1 9 23 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+++ /dev/null @@ -1,6 +0,0 @@ - - - - - - diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_macros.xml b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_macros.xml new file mode 120000 index 00000000..a6c33dbb --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_macros.xml @@ -0,0 +1 @@ +../fastx_macros.xml \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml index 17da76c5..4feb0f21 100644 --- a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml +++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml @@ -1,8 +1,9 @@ - + - - fastx_toolkit - + + + fastx_macros.xml + - - - - - diff --git a/tool_collections/fastx_toolkit/fastx_renamer/fastx_macros.xml b/tool_collections/fastx_toolkit/fastx_renamer/fastx_macros.xml new file mode 120000 index 00000000..a6c33dbb --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_renamer/fastx_macros.xml @@ -0,0 +1 @@ +../fastx_macros.xml \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml b/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml index 9db83ac9..c2e3f537 100644 --- a/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml +++ b/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml @@ -1,15 +1,16 @@ - + - - fastx_toolkit - + + + fastx_macros.xml + - + @@ -25,6 +26,11 @@ zcat -f < '$input' | fastx_renamer -n $TYPE -o '$output' -v + + + + + **What it does** diff --git a/tool_collections/fastx_toolkit/fastx_renamer/test-data/input.fastqsolexa b/tool_collections/fastx_toolkit/fastx_renamer/test-data/input.fastqsolexa new file mode 100644 index 00000000..6dd52e0c --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_renamer/test-data/input.fastqsolexa @@ -0,0 +1,4 @@ +@CSHL_4_FC042GAMMII_2_1_517_596 +GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT ++CSHL_4_FC042GAMMII_2_1_517_596 +40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40 \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastx_renamer/test-data/renamed_nt_sequence.fastqsolexa b/tool_collections/fastx_toolkit/fastx_renamer/test-data/renamed_nt_sequence.fastqsolexa new file mode 100644 index 00000000..2dfe3ffb --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_renamer/test-data/renamed_nt_sequence.fastqsolexa @@ -0,0 +1,4 @@ +@GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT +GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT ++GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT +40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40 diff --git a/tool_collections/fastx_toolkit/fastx_renamer/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_renamer/tool_dependencies.xml deleted file mode 100644 index 5474ad78..00000000 --- a/tool_collections/fastx_toolkit/fastx_renamer/tool_dependencies.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - - - diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_macros.xml b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_macros.xml new file mode 120000 index 00000000..a6c33dbb --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_macros.xml @@ -0,0 +1 @@ +../fastx_macros.xml \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml index 1dc46aed..9bd448de 100644 --- a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml @@ -1,15 +1,16 @@ - + - - fastx_toolkit - + + + fastx_macros.xml + - + diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_reverse_complement/tool_dependencies.xml deleted file mode 100644 index 5474ad78..00000000 --- a/tool_collections/fastx_toolkit/fastx_reverse_complement/tool_dependencies.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - - - diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_macros.xml b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_macros.xml new file mode 120000 index 00000000..a6c33dbb --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_macros.xml @@ -0,0 +1 @@ +../fastx_macros.xml \ No newline at end of file diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml index d6ebbc50..7f57d910 100644 --- a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml +++ b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml @@ -1,15 +1,16 @@ - + - - fastx_toolkit - + + + fastx_macros.xml + - + diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/tool_dependencies.xml b/tool_collections/fastx_toolkit/fastx_trimmer/tool_dependencies.xml deleted file mode 100644 index 5474ad78..00000000 --- a/tool_collections/fastx_toolkit/fastx_trimmer/tool_dependencies.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - - - From 8865acd57892fa9e683b603e361363fc8baebbc5 Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Sun, 18 Sep 2016 11:17:53 +0200 Subject: [PATCH 04/12] Explicitly set `-Q` for all non-cs fastq variants -Q 33 is the default, but it needs to be set to -Q 64 for fastqillumina and fastqsolexa. --- .../fasta_nucleotide_changer.xml | 6 +++--- .../fastq_quality_filter/fastq_quality_filter.xml | 15 +++++++++------ .../fastq_to_fasta/fastq_to_fasta.xml | 14 +++++++++----- .../fastx_artifacts_filter.xml | 14 ++++++++------ .../fastx_barcode_splitter.xml | 3 ++- .../fastx_toolkit/fastx_clipper/fastx_clipper.xml | 14 ++++++++------ .../fastx_collapser/fastx_collapser.xml | 14 ++++++++------ .../fastx_quality_statistics.xml | 13 +++++++++---- .../fastx_toolkit/fastx_renamer/fastx_renamer.xml | 14 ++++++++------ .../fastx_reverse_complement.xml | 14 ++++++++------ .../fastx_toolkit/fastx_trimmer/fastx_trimmer.xml | 14 ++++++++------ 11 files changed, 80 insertions(+), 55 deletions(-) diff --git a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml index 9f94eb60..1f256298 100644 --- a/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml +++ b/tool_collections/fastx_toolkit/fasta_nucleotide_changer/fasta_nucleotide_changer.xml @@ -5,9 +5,9 @@ fastx_macros.xml - + diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml b/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml index 8552b5d4..2d4c3d5d 100644 --- a/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml +++ b/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml @@ -5,12 +5,15 @@ fastx_macros.xml - + diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml index 82cdfa31..7cc953db 100644 --- a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml @@ -4,12 +4,16 @@ fastx_macros.xml - gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v - #if $input.ext == "fastqsanger": - -Q 33 - #end if + + - diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml b/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml index b7d55cc9..71a8d638 100644 --- a/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml +++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml @@ -5,12 +5,14 @@ fastx_macros.xml - + diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml index 39c009f2..90ede1f4 100644 --- a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml @@ -5,8 +5,9 @@ fastx_macros.xml + '$output' - + ]]> diff --git a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml index 493cc0fa..7f3bff08 100644 --- a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml +++ b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml @@ -5,12 +5,14 @@ fastx_macros.xml - + diff --git a/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml index 7e2b1015..92a3650e 100644 --- a/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml +++ b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml @@ -5,12 +5,14 @@ fastx_macros.xml - + diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml index 4feb0f21..f78d3491 100644 --- a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml +++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml @@ -5,13 +5,18 @@ fastx_macros.xml - + - + diff --git a/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml b/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml index c2e3f537..e24038bd 100644 --- a/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml +++ b/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml @@ -5,12 +5,14 @@ fastx_macros.xml - + diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml index 9bd448de..cc82411a 100644 --- a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml @@ -5,12 +5,14 @@ fastx_macros.xml - + diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml index 7f57d910..cb70824a 100644 --- a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml +++ b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml @@ -5,12 +5,14 @@ fastx_macros.xml - + From 0c1f99dfa678a33f95289c72e6fe057ed34545f7 Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Sun, 18 Sep 2016 11:30:03 +0200 Subject: [PATCH 05/12] Close command tag --- .../fastx_barcode_splitter/fastx_barcode_splitter.xml | 1 + 1 file changed, 1 insertion(+) diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml index 90ede1f4..88da87ff 100644 --- a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml @@ -8,6 +8,7 @@ '$output' ]]> + From f4e5d275e251ba73bb61e2bcb7e1058ced3923ac Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Sun, 18 Sep 2016 12:05:05 +0200 Subject: [PATCH 06/12] Fix command tag ... again --- .../fastx_barcode_splitter/fastx_barcode_splitter.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml index 88da87ff..baa28c1a 100644 --- a/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml +++ b/tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml @@ -6,7 +6,7 @@ '$output' + bash "$__tool_directory__"/fastx_barcode_splitter_galaxy_wrapper.sh '$BARCODE' '$input' "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > '$output' ]]> From f20670626fc0c57917b8530a5686c9ecf3dfc9a5 Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Sun, 18 Sep 2016 12:16:32 +0200 Subject: [PATCH 07/12] Fix requirements --- .../fastx_nucleotides_distribution.xml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml index 0d1abd22..c1659573 100644 --- a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml +++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml @@ -1,8 +1,9 @@ - - gnuplot - + + + fastx_macros.xml + fastx_macros.xml From 361f286c7067d3a05a934fdc43a141e759d4778c Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Sun, 18 Sep 2016 12:29:43 +0200 Subject: [PATCH 08/12] Don't fail with gnuplot warnings --- .../fastx_nucleotides_distribution.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml index c1659573..1dedc392 100644 --- a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml +++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml @@ -7,7 +7,7 @@ fastx_macros.xml - fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output + fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output From 0024992612d7f39d2823f97298fb4de848c14b4d Mon Sep 17 00:00:00 2001 From: Marius van den Beek Date: Sun, 18 Sep 2016 12:38:42 +0200 Subject: [PATCH 09/12] Use simsize comparison for png --- .../fastx_nucleotides_distribution.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml index 1dedc392..c0f0bea6 100644 --- a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml +++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml @@ -17,7 +17,7 @@ - + From 3fdc28dd5a676c5c1e7c790360b267bf86c8d574 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Sun, 1 Jan 2017 18:40:48 +0100 Subject: [PATCH 10/12] Retab certain fastx tools, remove duplicate macro imports --- .../fasta_clipping_histogram.xml | 3 -- .../fastq_quality_boxplot.xml | 34 +++++++++---------- .../fastx_nucleotides_distribution.xml | 31 ++++++++--------- 3 files changed, 31 insertions(+), 37 deletions(-) diff --git a/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml b/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml index 3fde9317..cf14f7fc 100644 --- a/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml +++ b/tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml @@ -4,9 +4,6 @@ fastx_macros.xml - - fastx_macros.xml - - + fastx_macros.xml - - fastq_quality_boxplot_graph.sh -t '$input.name' -i '$input' -o '$output' - - - - - - - - - - - - - - + + fastq_quality_boxplot_graph.sh -t '$input.name' -i '$input' -o '$output' + + + + + + + + + + + + + + **What it does** diff --git a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml index c0f0bea6..98cfa850 100644 --- a/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml +++ b/tool_collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml @@ -1,25 +1,22 @@ - + fastx_macros.xml - - fastx_macros.xml - - fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output - - - - - - - - - - - - + fastx_nucleotide_distribution_graph.sh -t '$input.name' -i '$input' -o '$output' + + + + + + + + + + + + **What it does** From d55db72b24cc86542881cdafbbe3b448ed621805 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Sun, 1 Jan 2017 18:47:44 +0100 Subject: [PATCH 11/12] Retab more fastx tools --- .../fastq_to_fasta/fastq_to_fasta.xml | 92 +++++++++---------- .../fastx_clipper/fastx_clipper.xml | 10 +- .../fastx_collapser/fastx_collapser.xml | 10 +- .../fastx_quality_statistics.xml | 10 +- .../fastx_renamer/fastx_renamer.xml | 10 +- .../fastx_reverse_complement.xml | 10 +- .../fastx_trimmer/fastx_trimmer.xml | 10 +- 7 files changed, 76 insertions(+), 76 deletions(-) diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml index 7cc953db..2bd56bd5 100644 --- a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml @@ -1,54 +1,54 @@ - converter from FASTX-toolkit + converter from FASTX-toolkit fastx_macros.xml - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml index 7f3bff08..2ef9d7f9 100644 --- a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml +++ b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml @@ -7,11 +7,11 @@ diff --git a/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml index 92a3650e..cdd2f44d 100644 --- a/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml +++ b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml @@ -7,11 +7,11 @@ diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml index f78d3491..2e637de0 100644 --- a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml +++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml @@ -7,11 +7,11 @@ diff --git a/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml b/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml index e24038bd..144d606f 100644 --- a/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml +++ b/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml @@ -7,11 +7,11 @@ diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml index cc82411a..368a4e2a 100644 --- a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml @@ -7,11 +7,11 @@ diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml index cb70824a..9258f0fa 100644 --- a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml +++ b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml @@ -7,11 +7,11 @@ From f9a5168726c1e9eef426f0045a1b67c7866b0d85 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Fri, 20 Jan 2017 11:03:08 +0100 Subject: [PATCH 12/12] Replace '.ext ==' pattern with is_of_type --- .../fastq_quality_filter/fastq_quality_filter.xml | 4 ++-- .../fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml | 4 ++-- .../fastx_artifacts_filter/fastx_artifacts_filter.xml | 4 ++-- .../fastx_toolkit/fastx_clipper/fastx_clipper.xml | 4 ++-- .../fastx_toolkit/fastx_collapser/fastx_collapser.xml | 4 ++-- .../fastx_quality_statistics/fastx_quality_statistics.xml | 4 ++-- .../fastx_toolkit/fastx_renamer/fastx_renamer.xml | 4 ++-- .../fastx_reverse_complement/fastx_reverse_complement.xml | 4 ++-- .../fastx_toolkit/fastx_trimmer/fastx_trimmer.xml | 4 ++-- 9 files changed, 18 insertions(+), 18 deletions(-) diff --git a/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml b/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml index 2d4c3d5d..f1875adf 100644 --- a/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml +++ b/tool_collections/fastx_toolkit/fastq_quality_filter/fastq_quality_filter.xml @@ -8,9 +8,9 @@ diff --git a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml index 2bd56bd5..0af01176 100644 --- a/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml +++ b/tool_collections/fastx_toolkit/fastq_to_fasta/fastq_to_fasta.xml @@ -7,9 +7,9 @@ diff --git a/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml b/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml index 71a8d638..5024af84 100644 --- a/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml +++ b/tool_collections/fastx_toolkit/fastx_artifacts_filter/fastx_artifacts_filter.xml @@ -7,9 +7,9 @@ diff --git a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml index 2ef9d7f9..9195a6c3 100644 --- a/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml +++ b/tool_collections/fastx_toolkit/fastx_clipper/fastx_clipper.xml @@ -7,9 +7,9 @@ diff --git a/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml index cdd2f44d..906e28ec 100644 --- a/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml +++ b/tool_collections/fastx_toolkit/fastx_collapser/fastx_collapser.xml @@ -7,9 +7,9 @@ diff --git a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml index 2e637de0..3715c39f 100644 --- a/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml +++ b/tool_collections/fastx_toolkit/fastx_quality_statistics/fastx_quality_statistics.xml @@ -7,9 +7,9 @@ diff --git a/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml b/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml index 144d606f..0382bc61 100644 --- a/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml +++ b/tool_collections/fastx_toolkit/fastx_renamer/fastx_renamer.xml @@ -7,9 +7,9 @@ diff --git a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml index 368a4e2a..859b7bb3 100644 --- a/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml +++ b/tool_collections/fastx_toolkit/fastx_reverse_complement/fastx_reverse_complement.xml @@ -7,9 +7,9 @@ diff --git a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml index 9258f0fa..2537f5d3 100644 --- a/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml +++ b/tool_collections/fastx_toolkit/fastx_trimmer/fastx_trimmer.xml @@ -7,9 +7,9 @@