diff --git a/tool_collections/taxonomy/gi2taxonomy/gi2taxonomy.xml b/tool_collections/taxonomy/gi2taxonomy/gi2taxonomy.xml index d0da3a9cc..d76757255 100644 --- a/tool_collections/taxonomy/gi2taxonomy/gi2taxonomy.xml +++ b/tool_collections/taxonomy/gi2taxonomy/gi2taxonomy.xml @@ -3,6 +3,9 @@ taxonomy + + gi2taxonomy + gi2taxonomy.py $input $giField $idField $out_file1 ${GALAXY_DATA_INDEX_DIR} diff --git a/tool_collections/taxonomy/kraken2tax/kraken2tax.xml b/tool_collections/taxonomy/kraken2tax/kraken2tax.xml index 60cdd392e..0a0cf4c26 100644 --- a/tool_collections/taxonomy/kraken2tax/kraken2tax.xml +++ b/tool_collections/taxonomy/kraken2tax/kraken2tax.xml @@ -4,6 +4,9 @@ gawk gb_taxonomy_tools + + kraken2tax + "${out_file}" diff --git a/tool_collections/taxonomy/lca_wrapper/lca.xml b/tool_collections/taxonomy/lca_wrapper/lca.xml index 11c3ac602..f2724faf2 100644 --- a/tool_collections/taxonomy/lca_wrapper/lca.xml +++ b/tool_collections/taxonomy/lca_wrapper/lca.xml @@ -1,46 +1,49 @@ - - taxonomy - + + taxonomy + + + lca1 + lca.py $input1 $out_file1 $rank_bound - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + - + - - - - + + + + @@ -53,48 +56,48 @@ - - - - - -**What it does** - -This tool identifies the lowest taxonomic rank for which a mategenomic sequencing read is diagnostic. It takes datasets produced by *Fetch Taxonomic Ranks* tool (aka Taxonomy format) as the input. - -------- - -**Example** - -Suppose you have two reads, **read_1** and **read_2**, with the following taxonomic profiles (scroll sideways to see the entire dataset):: - - read_1 1 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 genus1 subgenus1 species1 subspecies1 - read_1 2 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 genus2 subgenus2 species2 subspecies2 - read_2 3 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum3 subphylum3 superclass3 class3 subclass3 superorder3 order3 suborder3 superfamily3 family3 subfamily3 tribe3 subtribe3 genus3 subgenus3 species3 subspecies3 - read_2 4 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum4 subphylum4 superclass4 class4 subclass4 superorder4 order4 suborder4 superfamily4 family4 subfamily4 tribe4 subtribe4 genus4 subgenus4 species4 subspecies4 - -For **read_1** taxonomic labels are consistent until the genus level, where the taxonomy splits into two branches, one ending with *subspecies1* and the other with *subspecies2*. This implies **that the lowest taxomomic rank read_1 can identify is SUBTRIBE**. Similarly, read_2 is diagnostic up until the **superphylum** level. As a results the output of this tool will be:: - - read_1 2 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 n n n n - read_2 3 root superkingdom1 kingdom1 subkingdom1 superphylum1 n n n n n n n n n n n n n n n n n - -where, **n** means *EMPTY*. - --------- - -**What's up with the drop down?** - -Why do we need the *require the lowest rank to be at least* dropdown? Let's look at the above example again. Suppose you need to find only those reads that are diagnostic on at least phylum level. To do this you need to set the *require the lowest rank to be at least* to **phylum**. As a result your output will look like this:: - - read_1 2 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 n n n n - -.. class:: infomark - -Note, that **read_2** is now omitted as it matches two phyla (**phylum3** and **phylum4**) and therefore is not diagnostic (but rather cosmopolitan) on *phylum* level. - - - - - - - + + + + + +**What it does** + +This tool identifies the lowest taxonomic rank for which a mategenomic sequencing read is diagnostic. It takes datasets produced by *Fetch Taxonomic Ranks* tool (aka Taxonomy format) as the input. + +------- + +**Example** + +Suppose you have two reads, **read_1** and **read_2**, with the following taxonomic profiles (scroll sideways to see the entire dataset):: + + read_1 1 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 genus1 subgenus1 species1 subspecies1 + read_1 2 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 genus2 subgenus2 species2 subspecies2 + read_2 3 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum3 subphylum3 superclass3 class3 subclass3 superorder3 order3 suborder3 superfamily3 family3 subfamily3 tribe3 subtribe3 genus3 subgenus3 species3 subspecies3 + read_2 4 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum4 subphylum4 superclass4 class4 subclass4 superorder4 order4 suborder4 superfamily4 family4 subfamily4 tribe4 subtribe4 genus4 subgenus4 species4 subspecies4 + +For **read_1** taxonomic labels are consistent until the genus level, where the taxonomy splits into two branches, one ending with *subspecies1* and the other with *subspecies2*. This implies **that the lowest taxomomic rank read_1 can identify is SUBTRIBE**. Similarly, read_2 is diagnostic up until the **superphylum** level. As a results the output of this tool will be:: + + read_1 2 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 n n n n + read_2 3 root superkingdom1 kingdom1 subkingdom1 superphylum1 n n n n n n n n n n n n n n n n n + +where, **n** means *EMPTY*. + +-------- + +**What's up with the drop down?** + +Why do we need the *require the lowest rank to be at least* dropdown? Let's look at the above example again. Suppose you need to find only those reads that are diagnostic on at least phylum level. To do this you need to set the *require the lowest rank to be at least* to **phylum**. As a result your output will look like this:: + + read_1 2 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 n n n n + +.. class:: infomark + +Note, that **read_2** is now omitted as it matches two phyla (**phylum3** and **phylum4**) and therefore is not diagnostic (but rather cosmopolitan) on *phylum* level. + + + + + + + diff --git a/tool_collections/taxonomy/t2ps/t2ps_wrapper.xml b/tool_collections/taxonomy/t2ps/t2ps_wrapper.xml index 7b6513880..d025913b1 100644 --- a/tool_collections/taxonomy/t2ps/t2ps_wrapper.xml +++ b/tool_collections/taxonomy/t2ps/t2ps_wrapper.xml @@ -3,6 +3,9 @@ taxonomy + + t2ps + t2ps_wrapper.py $input $out_file1 $max_tree_level $font_size $max_leaves 1 diff --git a/tool_collections/taxonomy/t2t_report/t2t_report.xml b/tool_collections/taxonomy/t2t_report/t2t_report.xml index ca6cc99d2..67cab9e2a 100644 --- a/tool_collections/taxonomy/t2t_report/t2t_report.xml +++ b/tool_collections/taxonomy/t2t_report/t2t_report.xml @@ -3,6 +3,9 @@ taxonomy + + t2t_report + taxonomy2tree $input 0 /dev/null $out_file1 0 diff --git a/tools/cd_hit_dup/cd_hit_dup.xml b/tools/cd_hit_dup/cd_hit_dup.xml index 3aa3ee75a..75c2cc24a 100644 --- a/tools/cd_hit_dup/cd_hit_dup.xml +++ b/tools/cd_hit_dup/cd_hit_dup.xml @@ -5,6 +5,9 @@ cd-hit-auxtools + + cd-hit + @@ -122,4 +125,4 @@ cd-hit-dup provides a number of options to tune how the duplicates are removed:: 10.1093/bioinformatics/bts565 - \ No newline at end of file + diff --git a/tools/multispecies_orthologous_microsats/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml b/tools/multispecies_orthologous_microsats/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml index 9193a3c6c..f0b500c11 100755 --- a/tools/multispecies_orthologous_microsats/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml +++ b/tools/multispecies_orthologous_microsats/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml @@ -1,5 +1,8 @@ for multiple (>2) species alignments + + multispecies_orthologous_microsats + multispecies_MicrosatDataGenerator_interrupted_GALAXY.pl $input1 diff --git a/tools/quality_filter/quality_filter.xml b/tools/quality_filter/quality_filter.xml index 6c4820b5c..73d5b0c94 100644 --- a/tools/quality_filter/quality_filter.xml +++ b/tools/quality_filter/quality_filter.xml @@ -4,6 +4,9 @@ bx-python numpy + + qualityfilter + quality_filter.py $input