# HG changeset patch
# User iracooke
# Date 1433367888 14400
# Node ID 8d6c1807c5a5ca2e745b3f2af796029a286ff6d9
# Parent  843dba58aa7c69285443713a04d78d3c68ce8875
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit d369c3451aaf7bfc8cc4f6f1dc52f6ea604e66bc-dirty

diff -r 843dba58aa7c -r 8d6c1807c5a5 peptide_shaker.xml
--- a/peptide_shaker.xml	Wed Jun 03 17:11:02 2015 -0400
+++ b/peptide_shaker.xml	Wed Jun 03 17:44:48 2015 -0400
@@ -2,12 +2,12 @@
     <description>
         Perform protein identification using various search engines based on results from SearchGUI
     </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
     <requirements>
         <requirement type="package" version="0.39">peptide_shaker</requirement>
     </requirements>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
     <expand macro="stdio" />
     <command>
 <![CDATA[
diff -r 843dba58aa7c -r 8d6c1807c5a5 searchgui.xml
--- a/searchgui.xml	Wed Jun 03 17:11:02 2015 -0400
+++ b/searchgui.xml	Wed Jun 03 17:44:48 2015 -0400
@@ -2,12 +2,12 @@
     <description>
         Perform protein identification using various search engines and prepare results for input to Peptide Shaker
     </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
     <requirements>
         <requirement type="package" version="1.28">searchgui</requirement>
     </requirements>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
     <expand macro="stdio" />
     <command>
 <![CDATA[
@@ -140,7 +140,7 @@
     			 -ms_amanda_instrument ${ms_amanda.ms_amanda_instrument} 
     			 -ms_amanda_max_rank ${ms_amanda.ms_amanda_max_rank} 
     			 -ms_amanda_mono ${ms_amanda.ms_amanda_mono}
-            # end if
+            #end if
             
             #if $myrimatch.myrimatch_advanced == "yes"
                 -myrimatch_min_pep_length ${myrimatch.myrimatch_min_pep_length}