# HG changeset patch
# User iuc
# Date 1466890138 14400
# Node ID aa333a0a7d5a0a25837ea68e24cf0813352c0c76
# Parent  dbe3901aace21ec33b413228fa6668075ababb0f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393

diff -r dbe3901aace2 -r aa333a0a7d5a macros.xml
--- a/macros.xml	Wed Jun 15 06:25:01 2016 -0400
+++ b/macros.xml	Sat Jun 25 17:28:58 2016 -0400
@@ -117,11 +117,11 @@
         ln -s batch_1.genotypes_*onemap.tsv batch_1.genotypes.onemap.tsv &&
         ln -s batch_1.genotypes_*.onemap.txt batch_1.genotypes.onemap.txt &&
         ln -s batch_1.genomic_*.tsv batch_1.genomic.tsv &&
-        ln -s batch_1.genotypes_1.rqtl.tsv batch_1.genotypes.rqtl.tsv &&
-        ln -s batch_1.haplotypes_1.tsv batch_1.haplotypes.tsv &&
+        ln -s batch_1.genotypes_*.rqtl.tsv batch_1.genotypes.rqtl.tsv &&
+        ln -s batch_1.haplotypes_*.tsv batch_1.haplotypes.tsv &&
         ln -s batch_1.genotypes_*.loc batch_1.genotypes.loc &&
-        ln -s batch_1.genotypes_1.txt batch_1.genotypes.txt &&
-        ln -s batch_1.genotypes_1.tsv batch_1.genotypes.tsv &&
+        ln -s batch_1.genotypes_*.txt batch_1.genotypes.txt &&
+        ln -s batch_1.genotypes_*[^rqtl].tsv batch_1.genotypes.tsv &&
         cd ..
         ]]>
     </token>
diff -r dbe3901aace2 -r aa333a0a7d5a stacks_genotypes.xml
--- 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
diff -r dbe3901aace2 -r aa333a0a7d5a tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jun 15 06:25:01 2016 -0400
+++ b/tool_dependencies.xml	Sat Jun 25 17:28:58 2016 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="stacks" version="1.40">
-        <repository changeset_revision="95cffefc0dfe" name="package_stacks_1_40" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="51d4ab2c4dcf" name="package_stacks_1_40" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="velvet" version="1.2.10">
         <repository changeset_revision="93d32326537b" name="package_velvet_1_2_10" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />