Mercurial > repos > iuc > deseq2

diff deseq2.xml @ 12:bd06df00180a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 62e9101c1e7b8467e395f31ccbd9321de01a6418
author iuc
date Mon, 29 Jan 2018 07:30:18 -0500
parents 25204a860b79
children 3660c9088494
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--- a/deseq2.xml	Sun Jan 28 04:04:12 2018 -0500
+++ b/deseq2.xml	Mon Jan 29 07:30:18 2018 -0500
@@ -1,8 +1,10 @@
-<tool id="deseq2" name="DESeq2" version="2.11.40">
+<tool id="deseq2" name="DESeq2" version="2.11.40.1">
     <description>Determines differentially expressed features from count tables</description>
     <requirements>
         <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement>
         <requirement type="package" version="1.6.0">bioconductor-tximport</requirement>
+        <requirement type="package" version="0.6.5">r-ggrepel</requirement>
+        <requirement type="package" version="1.0.8">r-pheatmap</requirement>
     </requirements>
     <stdio>
         <regex match="Execution halted"
@@ -31,6 +33,7 @@
 #end if
 
 #import json
+#import os
 Rscript '${__tool_directory__}/deseq2.R'
     -o '$deseq_out'
     #if $pdf:
@@ -39,6 +42,7 @@
     #if $normCounts:
         -n '$counts_out'
     #end if
+    #set $filename_to_element_identifiers = {}
     #set $temp_factor_names = list()
     #for $factor in $rep_factorName:
         #set $temp_factor = list()
@@ -46,6 +50,7 @@
             #set $count_files = list()
             #for $file in $level.countsFile:
                 $count_files.append(str($file))
+                $filename_to_element_identifiers.__setitem__(os.path.basename(str($file)),  $file.element_identifier)
             #end for
             $temp_factor.append( {str($level.factorLevel): $count_files} )
         #end for
@@ -53,6 +58,7 @@
         $temp_factor_names.append([str($factor.factorName), $temp_factor])
     #end for
     -f '#echo json.dumps(temp_factor_names)#'
+    -l '#echo json.dumps(filename_to_element_identifiers)#'
     -t $fit_type
     #if $outlier_replace_off:
         -a