diff pangenomeCogAnalysis.xml @ 0:731fb6cb324b draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pangenomeCogAnalysis.xml	Wed Jun 30 13:30:19 2021 +0000
@@ -0,0 +1,40 @@
+<tool id="pangenome_cog_analysis" name="Pangenome COG Analysis" version="1.0">
+  <description>Provide statistics from pangenome matrix and COG annotations </description>
+ <!-- <requirements>
+  <requirement type="package" version=""></requirement>
+</requirements> -->
+    <command detect_errors="aggressive"><![CDATA[
+        #import re
+
+        ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
+        ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
+        #set $named_input_files = ''
+        #for $input_file in $input_files
+            ## Add single quotes around each input file identifier
+            #set $_input_file = "'{}'".format($input_file.element_identifier)
+            ln -s '${input_file}' ${_input_file} &&
+            #set $named_input_files = $named_input_files + ',' + $_input_file
+        #end for
+
+	perl ${__tool_directory__}/pangenomeCogAnalysis_V1.pl $input $input2 $named_input_files $input_files $gff_files order $output $output2 $output3 $output4 $output5
+	]]></command>
+
+
+
+  <inputs>
+  <param format="tabular" name="input" type="data" label="Pangenome Matrix" help="Headers must be: Cluster,genes_strain1,genes_strain2..."/>
+  <param format="tabular" name="input2" type="data" label="Strains group file (example species information)" help="Headers must be: strain1,groupinfo"/>
+  <param type="data" name="input_files" format="txt" multiple="true" label="Collection of COG files" help="Each files must be named with the same strain name as defined in Strain group file. Headers must be Gene,COG,COGcategory"/>
+  <param type="data" name="gff_files" format="gff3" multiple="true" label="Collection of GFF files for preparing Circos track" help="Not necessarily annotations from all strains, only those that you want to be represented as Circos tracks"/>
+  <!--<param format="tabular" name="input_files" type="data" multiple="true" label="Annotation files"/>-->
+ </inputs>
+
+ <outputs>
+	 <data format="txt" name="output" label="List of group-specific clusters"/>
+	 <data format="tabular" name="output2" label="COG category count average per group"/>
+	 <data format="tabular" name="output3" label="Detailed COG category count values per group"/>
+	 <data format="tabular" name="output4" label="COG category count average"/>
+	 <data format="tabular" name="output5" label="Core-genes coordinates"/>
+</outputs>
+
+</tool>