diff stacks_genotypes.xml @ 3:aa333a0a7d5a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393

--- a/stacks_genotypes.xml	Wed Jun 15 06:25:01 2016 -0400
+++ b/stacks_genotypes.xml	Sat Jun 25 17:28:58 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="stacks_genotypes" name="Stacks: genotypes" version="@WRAPPER_VERSION@.0">
+<tool id="stacks_genotypes" name="Stacks: genotypes" version="@WRAPPER_VERSION@.1">
     <description>analyse haplotypes or genotypes in a genetic cross ('genotypes' program)</description>
     <macros>
         <import>macros.xml</import>
@@ -6,17 +6,20 @@
     <expand macro="requirements"/>
     <expand macro="stdio"/>
     <command><![CDATA[
+        #import re
 
         mkdir stacks_outputs
 
         &&
 
         #for $input_file in $input_col:
-            #set $ext = ""
-            #if not str($input_file.name).endswith('.tsv'):
-                #set $ext = ".tsv"
+            #set $filename = str($input_file.element_identifier)
+            #if not $filename.endswith('.tsv'):
+                #set $filename = $filename + ".tsv"
             #end if
-            ln -s "${input_file}" "stacks_outputs/${input_file.name}${ext}" &&
+            #if re.search('\.(tags|snps|alleles|matches)(\.tsv)?$', $filename):
+                ln -s "${input_file}" "stacks_outputs/${filename}" &&
+            #end if
         #end for
 
         genotypes