# HG changeset patch
# User iuc
# Date 1466890072 14400
# Node ID 55814b6afe69e3dd5e1831e53043262ca00f9bb2
# Parent  77f5db79577429be1586abab9d0fd19a4f7f8964
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393

diff -r 77f5db795774 -r 55814b6afe69 macros.xml
--- a/macros.xml	Wed Jun 15 06:23:37 2016 -0400
+++ b/macros.xml	Sat Jun 25 17:27:52 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 77f5db795774 -r 55814b6afe69 stacks_rxstacks.xml
--- a/stacks_rxstacks.xml	Wed Jun 15 06:23:37 2016 -0400
+++ b/stacks_rxstacks.xml	Sat Jun 25 17:27:52 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="stacks_rxstacks" name="Stacks: rxstacks" version="@WRAPPER_VERSION@.0">
+<tool id="stacks_rxstacks" name="Stacks: rxstacks" version="@WRAPPER_VERSION@.1">
     <description>make corrections to genotype and haplotype calls</description>
     <macros>
         <import>macros.xml</import>
@@ -13,10 +13,10 @@
 
         #for $input_file in $input_col:
             #set $ext = ""
-            #if not str($input_file.name).endswith('.tsv'):
+            #if not str($input_file.element_identifier).endswith('.tsv'):
                 #set $ext = ".tsv"
             #end if
-            ln -s "${input_file}" "stacks_inputs/${input_file.name}${ext}" &&
+            ln -s "${input_file}" "stacks_inputs/${input_file.element_identifier}${ext}" &&
         #end for
 
         rxstacks
@@ -95,19 +95,19 @@
         </data>
 
         <collection name="tags" type="list" label="Assembled loci filtered from ${on_string}">
-            <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv" ext="tabular" directory="stacks_outputs" />
+            <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
         </collection>
 
         <collection name="snps" type="list" label="Model calls from each locus filtered from ${on_string}">
-            <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv" ext="tabular" directory="stacks_outputs" />
+            <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />
         </collection>
 
         <collection name="alleles" type="list" label="Haplotypes/alleles recorded from each locus filtered from ${on_string}">
-            <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv" ext="tabular" directory="stacks_outputs" />
+            <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
         </collection>
 
         <collection name="all_output" type="list" label="Full output from rxstacks on ${on_string}">
-            <discover_datasets pattern="(?P&lt;name&gt;.+\.(tags|snps|alleles))\.tsv" ext="tabular" directory="stacks_outputs" />
+            <discover_datasets pattern="(?P&lt;name&gt;.+\.(tags|snps|alleles))\.tsv$" ext="tabular" directory="stacks_outputs" />
         </collection>
     </outputs>
 
diff -r 77f5db795774 -r 55814b6afe69 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jun 15 06:23:37 2016 -0400
+++ b/tool_dependencies.xml	Sat Jun 25 17:27:52 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" />