# HG changeset patch
# User iuc
# Date 1575371927 18000
# Node ID 83f8b5ceff43451053ce3e3cf90c0326b494f31b
# Parent  db04ba860dabf7317bcd9d7941504a0292fe0044
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 60951bbe9b08fa6eb2762db9ee15c88e8acf1a1f"

diff -r db04ba860dab -r 83f8b5ceff43 masigpro.xml
--- a/masigpro.xml	Thu Jul 13 18:23:17 2017 -0400
+++ b/masigpro.xml	Tue Dec 03 06:18:47 2019 -0500
@@ -1,6 +1,7 @@
-<tool id="masigpro" name="maSigPro" version="1.49.3.1">
+<tool id="masigpro" name="maSigPro" version="1.49.3.1+galaxy1">
     <description>Significant Gene Expression Profile Differences in Time Course Gene Expression Data</description>
     <requirements>
+        <requirement type="package" version="8.25">coreutils</requirement>
         <requirement type="package" version="1.49.3">bioconductor-masigpro</requirement>
         <requirement type="package" version="1.3.2">r-optparse</requirement>
         <requirement type="package" version="4.4">sed</requirement>
@@ -42,7 +43,7 @@
         #end for
         > data && sed -i '1i$header' data &&
         #if $source.enable_output:
-            ln -f data $data_out && ln -f $design_matrix $edesign_out &&
+            cp $design_matrix $edesign_out &&
         #end if
         #set $data = 'data'
         #set $edesign = $design_matrix
@@ -85,6 +86,9 @@
         --cexlab $pdf.seeGenes.cexlab
         --legend $pdf.seeGenes.legend
     #end if
+    #if str($source.source_selector) == "advanced" and $source.enable_output
+        && mv data $data_out
+    #end if
     ]]>
     </command>
     <configfiles>