data_manager_cat: data_manager/macros.xml comparison

comparison data_manager/macros.xml @ 1:2bec6d7877fc draft default tip

planemo upload commit 68dbaa3df00fe628b7dc0310cd1d19605d0bb307-dirty

author	jjohnson
date	Tue, 26 Nov 2019 16:11:24 -0500
parents	f59e7e242bde
children

comparison

equal deleted inserted replaced

-:f59e7e242bde
+:2bec6d7877fc
 <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">
+<options from_data_table="cat_database">
 <filter type="sort_by" column="2" />
 <validator type="no_options" message="No CAT database is available." />
 </options>
 </param>
 </when>
 --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[
 <when value="both">
 <expand macro="add_names_options"/>
 </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">
 <param name="summarise" type="select" label="summarise">
 <option value="no">No</option>
 <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
+#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
 -o $summary_input
 #end if
 #if $bcat == 'CAT'
 -c $contigs_fasta
 #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 $classification_summary
 #end if
 ]]></token>
 <xml name="select_outputs">
 <param name="select_outputs" type="select" multiple="true" optional="false" label="Select outputs">
-<option value="log" selected="true">CAT.log</option>
+<option value="log" selected="true">log</option>
 <option value="predicted_proteins_faa" selected="true">predicted_proteins.faa</option>
 <option value="predicted_proteins_gff">predicted_proteins.gff</option>
 <option value="alignment_diamond">alignment.diamond</option>
 <option value="orf2lca" selected="true">ORF2LCA.txt</option>
 <yield/>
 </param>
 </xml>
 <xml name="select_cat_outputs">
 <param name="bcat" type="hidden" value="CAT"/>
 <param name="seqtype" type="hidden" value="contig"/>
+<param name="sum_titles" type="hidden" value="contigs,number of ORFs,number of positions"/>
+<param name="bin_col" type="hidden" value=""/>
 <expand macro="select_outputs">
 <option value="contig2classification" selected="true">contig2classification.txt</option>
 </expand>
 </xml>
 <xml name="select_bat_outputs">
 <param name="bcat" type="hidden" value="BAT"/>
 <param name="seqtype" type="hidden" value="bin"/>
+<param name="sum_titles" type="hidden" value="bins"/>
+<param name="bin_col" type="hidden" value="bin,"/>
 <expand macro="select_outputs">
 <option value="bin2classification" selected="true">bin2classification.txt</option>
 </expand>
 </xml>
-<token name="@TXT2TSV@"><![CDATA[
-$__tool_directory__/tabpad.py
-]]></token>
 <xml name="outputs">
 <data name="log" format="txt" label="${bcat}.log" from_work_dir="cat_output.log">
 <filter>'log' in select_outputs or not select_outputs</filter>
 </data>
 <data name="predicted_proteins_faa" format="fasta" label="${bcat}.predicted_proteins.faa" from_work_dir="cat_output.predicted_proteins.faa">
 </data>
 <data name="orf2lca" format="tabular" label="${bcat}.ORF2LCA.txt" from_work_dir="cat_output.ORF2LCA.tsv">
 <filter>'orf2lca' in select_outputs</filter>
 <actions>
 <action name="comment_lines" type="metadata" default="1" />
-<action name="column_names" type="metadata" default="ORF,lineage,bit-score" />
+<action name="column_names" type="metadata" default="ORF,${bin_col}lineage,bit-score" />
 </actions>
 </data>
 <data name="contig2classification" format="tabular" label="${bcat}.contig2classification.txt" from_work_dir="cat_output.contig2classification.tsv">
 <filter>'contig2classification' in select_outputs</filter>
 <actions>
 <action name="comment_lines" type="metadata" default="1" />
 <action name="column_names" type="metadata" default="bin,classification,reason,lineage,lineage scores" />
 </actions>
 </data>
 <data name="orf2lca_names" format="tabular" label="${bcat}.ORF2LCA.names.txt">
-<filter>'orf2lca' in names.add_names</filter>
+<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" />
 </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="comment_lines" type="metadata" default="4" />
-<action name="column_names" type="metadata" default="rank,clade,number of contigs,number of ORFs,number of positions" />
+<action name="column_names" type="metadata" default="rank,clade,number of ${sum_titles}" />
 </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>
+<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>
 </macros>

Mercurial > repos > jjohnson > data_manager_cat

comparison data_manager/macros.xml @ 1:2bec6d7877fc draft default tip