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Update RSEM #610

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Update RSEM #610

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e955182
Update_rsem
gallardoalba Jan 3, 2023
863ab6a
Update purged GTF output teste
gallardoalba Mar 1, 2023
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2 changes: 1 addition & 1 deletion tools/rsem/macros.xml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
<?xml version="1.0"?>
<macros>
<token name="@WRAPPER_VERSION@">1.0.1</token>
<token name="@WRAPPER_VERSION@">1.0.2</token>
<xml name="requirements">
<requirements>
<requirement type="package" version="1.3.0=pl526r341h4f16992_4">rsem</requirement>
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12 changes: 9 additions & 3 deletions tools/rsem/rsem.xml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
<tool id="rsembowtie" name="RSEM-Bowtie" version="@WRAPPER_VERSION@">
<description></description>
<tool id="rsem" name="RSEM" version="@WRAPPER_VERSION@">
<description>quantification of gene and isoform expression from RNA-Seq data</description>
<macros>
<import>macros.xml</import>
</macros>
Expand All @@ -26,7 +26,7 @@
#if $job.transcript_to_gene_map:
--transcript-to-gene-map $job.transcript_to_gene_map
#end if
--bowtie
$aligner_tool
#if $job.self_reference.ref_type == 'transcripts':
$job.self_reference.reference_fasta_file
#else:
Expand Down Expand Up @@ -158,6 +158,12 @@
]]></command>

<inputs>
<param name="aligner_tool" type="select" label="Aligner tool to use" help="TODO">
<option value="--bowtie">Bowtie</option>
<option value="--bowtie2">Bowtie2</option>
<option value="--hisat2-hca">HISAT2</option>
<option value="--star">RNASTAR</option>
</param>
<conditional name="job">
<param name="select_job" type="select" label="rsem reference">
<option value="index">Build rsem reference</option>
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102 changes: 51 additions & 51 deletions tools/rsem/test-data/purged.gtf.log
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Original file line number Diff line number Diff line change
@@ -1,62 +1,62 @@
NM_001145149.2"; transcript_id "NM_001145149.2"; chrY,chrX
NM_006883.2"; transcript_id "NM_006883.2"; chrY,chrX
NM_004192.3"; transcript_id "NM_004192.3"; chrY,chrX
NM_001173474.1"; transcript_id "NM_001173474.1"; chrY,chrX
NM_001173473.1"; transcript_id "NM_001173473.1"; chrY,chrX
NM_145177.2"; transcript_id "NM_145177.2"; chrY,chrX
NM_001171135.1"; transcript_id "NM_001171135.1"; chrY,chrX
NM_001171136.1"; transcript_id "NM_001171136.1"; chrY,chrX
NM_004729.3"; transcript_id "NM_004729.3"; chrY,chrX
NR_033381.1"; transcript_id "NR_033381.1"; chrY,chrX
NR_033380.1"; transcript_id "NR_033380.1"; chrY,chrX
NM_001304990.1"; transcript_id "NM_001304990.1"; chrY,chrX
NR_028057.1"; transcript_id "NR_028057.1"; chrY,chrX
NM_018390.3"; transcript_id "NM_018390.3"; chrY,chrX
NM_012227.3"; transcript_id "NM_012227.3"; chrY,chrX
NR_027231.1"; transcript_id "NR_027231.1"; chrY,chrX
NR_027232.1"; transcript_id "NR_027232.1"; chrY,chrX
NM_172247.2"; transcript_id "NM_172247.2"; chrY,chrX
NR_037461.1"; transcript_id "NR_037461.1"; chrY,chrX
NM_013239.4"; transcript_id "NM_013239.4"; chrY,chrX
NM_000451.3"; transcript_id "NM_000451.3"; chrY,chrX
NM_022148.3"; transcript_id "NM_022148.3"; chrY,chrX
NR_110830.1"; transcript_id "NR_110830.1"; chrY,chrX
NM_001012288.2"; transcript_id "NM_001012288.2"; chrY,chrX
NM_001161531.1"; transcript_id "NM_001161531.1"; chrY,chrX
NR_027760.1"; transcript_id "NR_027760.1"; chrY,chrX
NR_033714.1"; transcript_id "NR_033714.1"; chrY,chrX
NM_004043.2"; transcript_id "NM_004043.2"; chrY,chrX
NM_001171135.1"; transcript_id "NM_001171135.1"; chrY,chrX
NM_172249.2"; transcript_id "NM_172249.2"; chrY,chrX
NR_033715.1"; transcript_id "NR_033715.1"; chrY,chrX
NM_001161532.1"; transcript_id "NM_001161532.1"; chrY,chrX
NM_172245.2"; transcript_id "NM_172245.2"; chrY,chrX
NM_001267713.1"; transcript_id "NM_001267713.1"; chrY,chrX
NM_001171039.1"; transcript_id "NM_001171039.1"; chrY,chrX
NM_001161529.1"; transcript_id "NM_001161529.1"; chrY,chrX
NM_172249.2"; transcript_id "NM_172249.2"; chrY,chrX
NR_027760.1"; transcript_id "NR_027760.1"; chrY,chrX
NM_172246.2"; transcript_id "NM_172246.2"; chrY,chrX
NR_033380.1"; transcript_id "NR_033380.1"; chrY,chrX
NM_001321368.1"; transcript_id "NM_001321368.1"; chrY,chrX
NM_001173474.1"; transcript_id "NM_001173474.1"; chrY,chrX
NM_001012288.2"; transcript_id "NM_001012288.2"; chrY,chrX
NM_001321370.1"; transcript_id "NM_001321370.1"; chrY,chrX
NR_135623.1"; transcript_id "NR_135623.1"; chrY,chrX
NM_022148.3"; transcript_id "NM_022148.3"; chrY,chrX
NM_012227.3"; transcript_id "NM_012227.3"; chrY,chrX
NM_005638.5"; transcript_id "NM_005638.5"; chrY,chrX
NM_001171038.1"; transcript_id "NM_001171038.1"; chrY,chrX
NM_005088.2"; transcript_id "NM_005088.2"; chrY,chrX
NM_001173473.1"; transcript_id "NM_001173473.1"; chrY,chrX
NM_001636.3"; transcript_id "NM_001636.3"; chrY,chrX
NM_006140.4"; transcript_id "NM_006140.4"; chrY,chrX
NM_172247.2"; transcript_id "NM_172247.2"; chrY,chrX
NM_001161530.1"; transcript_id "NM_001161530.1"; chrY,chrX
NR_037461.1"; transcript_id "NR_037461.1"; chrY,chrX
NM_001267713.1"; transcript_id "NM_001267713.1"; chrY,chrX
NM_002183.3"; transcript_id "NM_002183.3"; chrY,chrX
NR_037842.1"; transcript_id "NR_037842.1"; chrY,chrX
NM_006883.2"; transcript_id "NM_006883.2"; chrY,chrX
NM_004192.3"; transcript_id "NM_004192.3"; chrY,chrX
NR_106737.1"; transcript_id "NR_106737.1"; chrY,chrX
NR_026710.1"; transcript_id "NR_026710.1"; chrY,chrX
NM_001161532.1"; transcript_id "NM_001161532.1"; chrY,chrX
NM_002414.4"; transcript_id "NM_002414.4"; chrY,chrX
NM_145177.2"; transcript_id "NM_145177.2"; chrY,chrX
NM_001636.3"; transcript_id "NM_001636.3"; chrY,chrX
NR_130733.1"; transcript_id "NR_130733.1"; chrY,chrX
NR_110561.1"; transcript_id "NR_110561.1"; chrY,chrX
NM_176786.1"; transcript_id "NM_176786.1"; chrY,chrX
NR_033381.1"; transcript_id "NR_033381.1"; chrY,chrX
NR_027231.1"; transcript_id "NR_027231.1"; chrY,chrX
NM_001161529.1"; transcript_id "NM_001161529.1"; chrY,chrX
NM_000451.3"; transcript_id "NM_000451.3"; chrY,chrX
NM_004729.3"; transcript_id "NM_004729.3"; chrY,chrX
NM_013239.4"; transcript_id "NM_013239.4"; chrY,chrX
NR_026710.1"; transcript_id "NR_026710.1"; chrY,chrX
NR_026711.1"; transcript_id "NR_026711.1"; chrY,chrX
NM_001161530.1"; transcript_id "NM_001161530.1"; chrY,chrX
NR_027383.1"; transcript_id "NR_027383.1"; chrY,chrX
NR_028057.1"; transcript_id "NR_028057.1"; chrY,chrX
NR_110830.1"; transcript_id "NR_110830.1"; chrY,chrX
NM_002186.2"; transcript_id "NM_002186.2"; chrY,chrX
NM_001122898.2"; transcript_id "NM_001122898.2"; chrY,chrX
NM_178129.4"; transcript_id "NM_178129.4"; chrY,chrX
NM_001185183.1"; transcript_id "NM_001185183.1"; chrY,chrX
NM_001321369.1"; transcript_id "NM_001321369.1"; chrY,chrX
NM_018390.3"; transcript_id "NM_018390.3"; chrY,chrX
NM_001304990.1"; transcript_id "NM_001304990.1"; chrY,chrX
NR_027383.1"; transcript_id "NR_027383.1"; chrY,chrX
NM_005088.2"; transcript_id "NM_005088.2"; chrY,chrX
NM_004043.2"; transcript_id "NM_004043.2"; chrY,chrX
NM_001171038.1"; transcript_id "NM_001171038.1"; chrY,chrX
NM_001171039.1"; transcript_id "NM_001171039.1"; chrY,chrX
NR_106737.1"; transcript_id "NR_106737.1"; chrY,chrX
NR_037842.1"; transcript_id "NR_037842.1"; chrY,chrX
NM_001321367.1"; transcript_id "NM_001321367.1"; chrY,chrX
NM_001321369.1"; transcript_id "NM_001321369.1"; chrY,chrX
NM_001122898.2"; transcript_id "NM_001122898.2"; chrY,chrX
NM_001321370.1"; transcript_id "NM_001321370.1"; chrY,chrX
NM_001321368.1"; transcript_id "NM_001321368.1"; chrY,chrX
NM_002414.4"; transcript_id "NM_002414.4"; chrY,chrX
NR_135623.1"; transcript_id "NR_135623.1"; chrY,chrX
NM_005840.2"; transcript_id "NM_005840.2"; chrY,chrX
NM_001171136.1"; transcript_id "NM_001171136.1"; chrY,chrX
NM_001145149.2"; transcript_id "NM_001145149.2"; chrY,chrX
NR_033715.1"; transcript_id "NR_033715.1"; chrY,chrX
NR_033714.1"; transcript_id "NR_033714.1"; chrY,chrX
NM_001185183.1"; transcript_id "NM_001185183.1"; chrY,chrX
NM_005638.5"; transcript_id "NM_005638.5"; chrY,chrX
NM_002186.2"; transcript_id "NM_002186.2"; chrY,chrX
NM_176786.1"; transcript_id "NM_176786.1"; chrY,chrX
NR_110561.1"; transcript_id "NR_110561.1"; chrY,chrX
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