# HG changeset patch
# User iuc
# Date 1466890163 14400
# Node ID 11642e18f2b0013fc83b5aba6c4f3815d575209a
# Parent  5d12647ff71f674f856765345879db8345610522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393

diff -r 5d12647ff71f -r 11642e18f2b0 macros.xml
--- a/macros.xml	Wed Jun 15 06:25:27 2016 -0400
+++ b/macros.xml	Sat Jun 25 17:29:23 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 5d12647ff71f -r 11642e18f2b0 stacks_procrad.xml
--- a/stacks_procrad.xml	Wed Jun 15 06:25:27 2016 -0400
+++ b/stacks_procrad.xml	Sat Jun 25 17:29:23 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="stacks_procrad" name="Stacks: process radtags" version="@WRAPPER_VERSION@.1">
+<tool id="stacks_procrad" name="Stacks: process radtags" version="@WRAPPER_VERSION@.2">
 <description>the Stacks demultiplexing script</description>
     <macros>
         <import>macros.xml</import>
@@ -149,18 +149,18 @@
         <data format="txt" name="output_log" label="results.log with ${tool.name} on ${on_string}: demultiplexed and cleaned reads" from_work_dir="stacks_outputs/process_radtags.log" />
 
         <collection name="demultiplexed" type="list" label="Demultiplexed reads from ${on_string}">
-            <discover_datasets pattern="(?P&lt;name&gt;.+(\.[12])?)\.fq" ext="fastqsanger" directory="stacks_outputs" />
-            <discover_datasets pattern="(?P&lt;name&gt;.+(\.[12])?)\.fa" ext="fasta" directory="stacks_outputs" />
+            <discover_datasets pattern="(?P&lt;name&gt;.+(\.[12])?)\.fq$" ext="fastqsanger" directory="stacks_outputs" />
+            <discover_datasets pattern="(?P&lt;name&gt;.+(\.[12])?)\.fa$" ext="fasta" directory="stacks_outputs" />
         </collection>
         <collection name="remaining" type="list" label="Remaining orphan reads from ${on_string}">
             <filter>input_type['options_type_selector'] == "paired"</filter>
-            <discover_datasets pattern="(?P&lt;name&gt;.+\.rem(\.[12])?)\.fq" ext="fastqsanger" directory="stacks_outputs" />
-            <discover_datasets pattern="(?P&lt;name&gt;.+\.rem(\.[12])?)\.fa" ext="fasta" directory="stacks_outputs" />
+            <discover_datasets pattern="(?P&lt;name&gt;.+\.rem(\.[12])?)\.fq$" ext="fastqsanger" directory="stacks_outputs" />
+            <discover_datasets pattern="(?P&lt;name&gt;.+\.rem(\.[12])?)\.fa$" ext="fasta" directory="stacks_outputs" />
         </collection>
         <collection name="discarded" type="list" label="${tool.name}: discarded reads from ${on_string}">
             <filter>capture is True</filter>
-            <discover_datasets pattern="(?P&lt;name&gt;.+)\.fq\.discards" ext="fastqsanger" directory="stacks_outputs" />
-            <discover_datasets pattern="(?P&lt;name&gt;.+)\.fa\.discards" ext="fasta" directory="stacks_outputs" />
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.fq\.discards$" ext="fastqsanger" directory="stacks_outputs" />
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.fa\.discards$" ext="fasta" directory="stacks_outputs" />
         </collection>
     </outputs>
 
diff -r 5d12647ff71f -r 11642e18f2b0 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jun 15 06:25:27 2016 -0400
+++ b/tool_dependencies.xml	Sat Jun 25 17:29:23 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" />