Mercurial > repos > jjohnson > data_manager_cat
changeset 1:2bec6d7877fc draft default tip
planemo upload commit 68dbaa3df00fe628b7dc0310cd1d19605d0bb307-dirty
| author | jjohnson |
|---|---|
| date | Tue, 26 Nov 2019 16:11:24 -0500 |
| parents | f59e7e242bde |
| children | |
| files | data_manager/macros.xml |
| diffstat | 1 files changed, 21 insertions(+), 19 deletions(-) [+] |
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--- a/data_manager/macros.xml Sun Nov 24 21:54:57 2019 -0500 +++ b/data_manager/macros.xml Tue Nov 26 16:11:24 2019 -0500 @@ -19,7 +19,7 @@ </param> <when value="cached"> <param name="cat_builtin" type="select" label="Use a built-in CAT database" help="If the CAT database of interest is not listed, contact your Galaxy administrator"> - <options from_data_table="cat_databases"> + <options from_data_table="cat_database"> <filter type="sort_by" column="2" /> <validator type="no_options" message="No CAT database is available." /> </options> @@ -77,7 +77,6 @@ #end if --out_prefix 'cat_output' ]]></token> - <xml name="custom_settings"> <param argument="--range" type="integer" value="10" min="0" max="49" label="range"/> <param argument="--fraction" type="float" value="0.5" min="0" max="0.99" label="fraction"/> @@ -115,24 +114,25 @@ </when> </conditional> </xml> + <token name="@TXT2TSV@">${__tool_directory__}/tabpad.py</token> <token name="@ADD_NAMES@"><![CDATA[ #if $names.add_names in ['classification','both']: && CAT add_names $names.only_official $names.exclude_scores @CAT_TAXONOMY@ #if $bcat == 'CAT' - -i cat_output.contigs2classification.tsv + -i cat_output.contig2classification.tsv #else -i cat_output.bin2classification.tsv #end if -o classification_names.txt - && @TXT2TSV@ -i classification_names -o $classification_names + && ${__tool_directory__}/tabpad.py -i classification_names.txt -o $classification_names #end if #if $names.add_names in ['orf2lca','both']: && CAT add_names $names.only_official $names.exclude_scores @CAT_TAXONOMY@ -i cat_output.ORF2LCA.tsv -o orf2lca_names.txt - && @TXT2TSV@ -i orf2lca_names.txt -o $orf2lca_names + && ${__tool_directory__}/tabpad.py -i orf2lca_names.txt -o $orf2lca_names #end if ]]></token> <xml name="summarise"> @@ -146,11 +146,11 @@ #if $names.add_names in ['classification','both'] and $names.only_official: #set $summary_input = $classification_names #else - #set $summary_input = classification_offical_names + #set $summary_input = 'classification_offical_names' && CAT add_names --only_official @CAT_TAXONOMY@ #if $bcat == 'CAT' - -i cat_output.contigs2classification.tsv + -i cat_output.contig2classification.tsv #else -i cat_output.bin2classification.tsv #end if @@ -162,13 +162,13 @@ #end if -i $summary_input -o classification_summary.txt - && @TXT2TSV@ -i classification_summary.txt -o $classification_summary + && ${__tool_directory__}/tabpad.py -i classification_summary.txt -o $classification_summary #end if ]]></token> <xml name="select_outputs"> <param name="select_outputs" type="select" multiple="true" optional="false" label="Select outputs"> - <option value="log" selected="true">CAT.log</option> + <option value="log" selected="true">log</option> <option value="predicted_proteins_faa" selected="true">predicted_proteins.faa</option> <option value="predicted_proteins_gff">predicted_proteins.gff</option> <option value="alignment_diamond">alignment.diamond</option> @@ -179,6 +179,8 @@ <xml name="select_cat_outputs"> <param name="bcat" type="hidden" value="CAT"/> <param name="seqtype" type="hidden" value="contig"/> + <param name="sum_titles" type="hidden" value="contigs,number of ORFs,number of positions"/> + <param name="bin_col" type="hidden" value=""/> <expand macro="select_outputs"> <option value="contig2classification" selected="true">contig2classification.txt</option> </expand> @@ -186,14 +188,12 @@ <xml name="select_bat_outputs"> <param name="bcat" type="hidden" value="BAT"/> <param name="seqtype" type="hidden" value="bin"/> + <param name="sum_titles" type="hidden" value="bins"/> + <param name="bin_col" type="hidden" value="bin,"/> <expand macro="select_outputs"> <option value="bin2classification" selected="true">bin2classification.txt</option> </expand> </xml> - - <token name="@TXT2TSV@"><![CDATA[ - $__tool_directory__/tabpad.py -]]></token> <xml name="outputs"> <data name="log" format="txt" label="${bcat}.log" from_work_dir="cat_output.log"> <filter>'log' in select_outputs or not select_outputs</filter> @@ -215,7 +215,7 @@ <filter>'orf2lca' in select_outputs</filter> <actions> <action name="comment_lines" type="metadata" default="1" /> - <action name="column_names" type="metadata" default="ORF,lineage,bit-score" /> + <action name="column_names" type="metadata" default="ORF,${bin_col}lineage,bit-score" /> </actions> </data> <data name="contig2classification" format="tabular" label="${bcat}.contig2classification.txt" from_work_dir="cat_output.contig2classification.tsv"> @@ -233,14 +233,14 @@ </actions> </data> <data name="orf2lca_names" format="tabular" label="${bcat}.ORF2LCA.names.txt"> - <filter>'orf2lca' in names.add_names</filter> + <filter>names['add_names'] in ['both','orf2lca']</filter> <actions> <action name="comment_lines" type="metadata" default="1" /> - <action name="column_names" type="metadata" default="ORF,lineage,bit-score,superkingdom,phylum,class,order,family,genus,species" /> + <action name="column_names" type="metadata" default="ORF,${bin_col}lineage,bit-score,superkingdom,phylum,class,order,family,genus,species" /> </actions> </data> <data name="classification_names" format="tabular" label="${bcat}.${seqtype}2classification.names.txt"> - <filter>'classification' in names.add_names</filter> + <filter>names['add_names'] in ['both','classification']</filter> <actions> <action name="comment_lines" type="metadata" default="1" /> <action name="column_names" type="metadata" default="${seqtype},classification,reason,lineage,lineage scores,superkingdom,phylum,class,order,family,genus,species" /> @@ -249,8 +249,8 @@ <data name="classification_summary" format="tabular" label="${bcat}.${seqtype}2classification.summary.txt"> <filter>'classification' in summarise</filter> <actions> - <action name="comment_lines" type="metadata" default="1" /> - <action name="column_names" type="metadata" default="rank,clade,number of contigs,number of ORFs,number of positions" /> + <action name="comment_lines" type="metadata" default="4" /> + <action name="column_names" type="metadata" default="rank,clade,number of ${sum_titles}" /> </actions> </data> </xml> @@ -261,6 +261,8 @@ <citations> <citation type="doi">https://doi.org/10.1101/072868</citation> <citation type="doi">https://doi.org/10.1186/s13059-019-1817-x</citation> + <citation type="doi">https://doi.org/10.1038/nmeth.3176</citation> + <citation type="doi">https://doi.org/10.1186/1471-2105-11-119</citation> <yield /> </citations> </xml>