Mercurial > repos > proteore > proteore_prot_features

diff prot_features.xml @ 2:6659a32876ea draft

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planemo upload commit 74f72978b11230744b116d34fe3f2aa7934bf545-dirty
author proteore
date Tue, 27 Feb 2018 08:11:33 -0500
parents bfc679370c64
children 57657705cd70
line wrap: on
line diff
--- a/prot_features.xml	Fri Feb 16 04:06:16 2018 -0500
+++ b/prot_features.xml	Tue Feb 27 08:11:33 2018 -0500
@@ -3,6 +3,7 @@
 Annotate your protein list using features retrieved from neXtProt database.
 </description>
 <requirements>
+  <requirement type="package" version="3.4.1">R</requirement>
 </requirements>
 <stdio>
   <exit_code range="1:" />
@@ -11,13 +12,31 @@
 
   #if $inputtype.filetype == "copy_paste":
     
-      Rscript $__tool_directory__/protein_features.R --inputtype=copypaste --input='$inputtype.genelist' --nextprot=$__tool_directory__/result_nextprot.txt --column=c1 --argsP1='$Nextprot_params.P1' --argsP2='$Nextprot_params.P2' --argsP3='$Nextprot_params.P3' --type='$idtype' --output='$output' --header=None 
+      Rscript $__tool_directory__/protein_features.R 
+      --inputtype=copypaste 
+      --input='$inputtype.genelist' 
+      --nextprot=$__tool_directory__/tool-data/result_nextprot.txt 
+      --column=c1 --header=None
+      --argsP1='$Nextprot_params.P1' 
+      --argsP2='$Nextprot_params.P2' 
+      --argsP3='$Nextprot_params.P3' 
+      --type='$idtype' 
+      --output='$output'  
     
   #end if
 
   #if $inputtype.filetype == "file_all": 
   
-      Rscript $__tool_directory__/protein_features.R --inputtype=tabfile --input='$inputtype.genelist' --nextprot=$__tool_directory__/result_nextprot.txt --column='$inputtype.column' --argsP1='$Nextprot_params.P1' --argsP2='$Nextprot_params.P2' --argsP3='$Nextprot_params.P3' --type='$idtype' --output='$output' --header='$inputtype.header' 
+      Rscript $__tool_directory__/protein_features.R 
+      --inputtype=tabfile 
+      --input='$inputtype.genelist' 
+      --nextprot=$__tool_directory__/tool-data/result_nextprot.txt 
+      --column='$inputtype.column' --header='$inputtype.header'
+      --argsP1='$Nextprot_params.P1' 
+      --argsP2='$Nextprot_params.P2' 
+      --argsP3='$Nextprot_params.P3' 
+      --type='$idtype' 
+      --output='$output' 
 
   #end if
     
@@ -112,7 +131,7 @@
 
 **Authors**
 
-T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
+Lisa Peru, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
 
 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform