Mercurial > repos > jjohnson > contig_annotation_tool
diff macros.xml @ 0:ad7507073c3f draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
| author | jjohnson |
|---|---|
| date | Sun, 24 Nov 2019 21:56:00 -0500 |
| parents | |
| children | 9a01840eac52 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sun Nov 24 21:56:00 2019 -0500 @@ -0,0 +1,267 @@ +<macros> + <token name="@VERSION@">5.0.3</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">cat</requirement> + <yield/> + </requirements> + </xml> + <xml name="version_command"> + <version_command>CAT --version</version_command> + </xml> + <token name="@DATABASE_FOLDER@">CAT_database</token> + <token name="@TAXONOMY_FOLDER@">taxonomy</token> + <xml name="cat_db"> + <conditional name="db"> + <param name="db_src" type="select" label="CAT database from"> + <option value="cached">local cached database</option> + <option value="history">history</option> + </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"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No CAT database is available." /> + </options> + </param> + </when> + <when value="history"> + <param name="cat_db" type="data" format="txt" label="A history dataset from CAT prepare tool"/> + </when> + </conditional> + </xml> + <token name="@CAT_DB@"><![CDATA[ + #if $db.db_src == 'cached': + --database_folder $db.cat_builtin.fields.database_folder + --taxonomy_folder $db.cat_builtin.fields.taxonomy_folder + #else + #import os.path + #set $catdb = $db.cat_db.extra_files_path + --database_folder '$os.path.join($catdb,"@DATABASE_FOLDER@")' + --taxonomy_folder '$os.path.join($catdb,"@TAXONOMY_FOLDER@")' + #end if +]]></token> + <token name="@CAT_TAXONOMY@"><![CDATA[ + #if $db.db_src == 'cached': + --taxonomy_folder $db.cat_builtin.fields.taxonomy_folder + #else + #import os.path + #set $catdb = $db.cat_db.extra_files_path + --taxonomy_folder '$os.path.join($catdb,"@TAXONOMY_FOLDER@")' + #end if +]]></token> + <xml name="test_catdb"> + <conditional name="db"> + <param name="db_src" value="cached"/> + <param name="cat_builtin" value="CAT_prepare_test"/> + </conditional> + </xml> + + <xml name="use_intermediates"> + <conditional name="previous"> + <param name="use_previous" type="select" label="Use previous gene prediction and diamond alignment"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param argument="--proteins_fasta" type="data" format="fasta" label="predicted proteins fasta"/> + <param argument="--diamond_alignment" type="data" format="fasta" label="alignments file"/> + </when> + </conditional> + </xml> + <token name="@USE_INTERMEDIATES@"><![CDATA[ + #if $previous.use_previous == 'yes' + --proteins_fasta '$previous.proteins_fasta' + --diamond_alignment '$previous.diamond_alignment' + #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"/> + </xml> + <token name="@CUSTOM_SETTINGS@"><![CDATA[ + --range $range + --fraction $fraction +]]></token> + <xml name="add_names_options"> + <param argument="--only_official" type="boolean" truevalue="--only_official" falsevalue="" checked="true" + label="Only output official level names."/> + <param argument="--exclude_scores" type="boolean" truevalue="--exclude_scores" falsevalue="" checked="false" + label="Exclude bit-score support scores in the lineage."/> + </xml> + <token name="@ADD_NAMES_OPTIONS@"><![CDATA[ + $only_official $exclude_scores +]]></token> + <xml name="add_names"> + <conditional name="names"> + <param name="add_names" type="select" label="add_names"> + <option value="no">No</option> + <option value="orf2lca">ORF2LCA.txt</option> + <option value="classification">classification.txt</option> + <option value="both">ORF2LCA.txt and classification.txt</option> + </param> + <when value="no"/> + <when value="orf2lca"> + <expand macro="add_names_options"/> + </when> + <when value="classification"> + <expand macro="add_names_options"/> + </when> + <when value="both"> + <expand macro="add_names_options"/> + </when> + </conditional> + </xml> + <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 + #else + -i cat_output.bin2classification.tsv + #end if + -o classification_names.txt + && @TXT2TSV@ -i classification_names -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 + #end if +]]></token> + <xml name="summarise"> + <param name="summarise" type="select" label="summarise"> + <option value="no">No</option> + <option value="classification">classification.txt</option> + </param> + </xml> + <token name="@SUMMARISE@"><![CDATA[ + #if $summarise in ['classification']: + #if $names.add_names in ['classification','both'] and $names.only_official: + #set $summary_input = $classification_names + #else + #set $summary_input = classification_offical_names + && CAT add_names --only_official + @CAT_TAXONOMY@ + #if $bcat == 'CAT' + -i cat_output.contigs2classification.tsv + #else + -i cat_output.bin2classification.tsv + #end if + -o $summary_input + #end if + && CAT summarise + #if $bcat == 'CAT' + -c $contigs_fasta + #end if + -i $summary_input + -o classification_summary.txt + && @TXT2TSV@ -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="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> + <option value="orf2lca" selected="true">ORF2LCA.txt</option> + <yield/> + </param> + </xml> + <xml name="select_cat_outputs"> + <param name="bcat" type="hidden" value="CAT"/> + <param name="seqtype" type="hidden" value="contig"/> + <expand macro="select_outputs"> + <option value="contig2classification" selected="true">contig2classification.txt</option> + </expand> + </xml> + <xml name="select_bat_outputs"> + <param name="bcat" type="hidden" value="BAT"/> + <param name="seqtype" 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> + </data> + <data name="predicted_proteins_faa" format="fasta" label="${bcat}.predicted_proteins.faa" from_work_dir="cat_output.predicted_proteins.faa"> + <filter>'predicted_proteins_faa' in select_outputs</filter> + </data> + <data name="predicted_proteins_gff" format="gff" label="${bcat}.predicted_proteins.gff" from_work_dir="cat_output.predicted_proteins.gff"> + <filter>'predicted_proteins_gff' in select_outputs</filter> + </data> + <data name="alignment_diamond" format="tabular" label="${bcat}.alignment.diamond" from_work_dir="cat_output.alignment.diamond"> + <filter>'alignment_diamond' in select_outputs</filter> + <actions> + <action name="comment_lines" type="metadata" default="1" /> + <action name="column_names" type="metadata" default="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore" /> + </actions> + </data> + <data name="orf2lca" format="tabular" label="${bcat}.ORF2LCA.txt" from_work_dir="cat_output.ORF2LCA.tsv"> + <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" /> + </actions> + </data> + <data name="contig2classification" format="tabular" label="${bcat}.contig2classification.txt" from_work_dir="cat_output.contig2classification.tsv"> + <filter>'contig2classification' in select_outputs</filter> + <actions> + <action name="comment_lines" type="metadata" default="1" /> + <action name="column_names" type="metadata" default="contig,classification,reason,lineage,lineage scores" /> + </actions> + </data> + <data name="bin2classification" format="tabular" label="${bcat}.bin2classification.txt" from_work_dir="cat_output.bin2classification.tsv"> + <filter>'bin2classification' in select_outputs</filter> + <actions> + <action name="comment_lines" type="metadata" default="1" /> + <action name="column_names" type="metadata" default="bin,classification,reason,lineage,lineage scores" /> + </actions> + </data> + <data name="orf2lca_names" format="tabular" label="${bcat}.ORF2LCA.names.txt"> + <filter>'orf2lca' in names.add_names</filter> + <actions> + <action name="comment_lines" type="metadata" default="1" /> + <action name="column_names" type="metadata" default="ORF,lineage,bit-score,superkingdom,phylum,class,order,family,genus,species" /> + </actions> + </data> + <data name="classification_names" format="tabular" label="${bcat}.${seqtype}2classification.names.txt"> + <filter>'classification' in names.add_names</filter> + <actions> + <action name="comment_lines" type="metadata" default="1" /> + <action name="column_names" type="metadata" default="${seqtype},classification,reason,lineage,lineage scores,superkingdom,phylum,class,order,family,genus,species" /> + </actions> + </data> + <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" /> + </actions> + </data> + </xml> + <token name="@COMMON_HELP@"><![CDATA[ +The CAT/BAT workflow is described at: https://github.com/dutilh/CAT +]]></token> + <xml name="citations"> + <citations> + <citation type="doi">https://doi.org/10.1101/072868</citation> + <citation type="doi">https://doi.org/10.1186/s13059-019-1817-x</citation> + <yield /> + </citations> + </xml> +</macros>