# HG changeset patch
# User iuc
# Date 1466890051 14400
# Node ID fede8a808d3627e0e7e694fbd7da283a1632438a
# Parent  0f16a6c3008541a7a76481dd109f2bbe10d44315
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393

diff -r 0f16a6c30085 -r fede8a808d36 macros.xml
--- a/macros.xml	Wed Jun 15 06:23:05 2016 -0400
+++ b/macros.xml	Sat Jun 25 17:27:31 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 0f16a6c30085 -r fede8a808d36 stacks_pstacks.xml
--- a/stacks_pstacks.xml	Wed Jun 15 06:23:05 2016 -0400
+++ b/stacks_pstacks.xml	Sat Jun 25 17:27:31 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="stacks_pstacks" name="Stacks: pstacks" version="@WRAPPER_VERSION@.0">
+<tool id="stacks_pstacks" name="Stacks: pstacks" version="@WRAPPER_VERSION@.2">
     <description>find stacks from short reads mapped to a reference genome</description>
     <macros>
         <import>macros.xml</import>
@@ -14,12 +14,12 @@
         &&
 
         #if $sample.ext == "sam":
-            #set $data_path = splitext($sample.name)[0]
+            #set $data_path = splitext($sample.element_identifier)[0]
             #set $data_path = re.sub(r'\.1$', '', $data_path)
             #set $data_path = "stacks_inputs/" + $data_path + ".sam"
             #set inputype = "sam"
         #else:
-            #set $data_path = splitext($sample.name)[0]
+            #set $data_path = splitext($sample.element_identifier)[0]
             #set $data_path = re.sub(r'\.1$', '', $data_path)
             #set $data_path = "stacks_inputs/" + $data_path + ".bam"
             #set inputype = "bam"
@@ -58,8 +58,10 @@
 
             -o stacks_outputs
 
+             > pstacks.log 2>&1
+
             ## If input is in bam format, stacks will output gzipped files (no option to control this)
-            && gunzip stacks_outputs/*.gz
+            && if ls stacks_outputs/*.gz > /dev/null 2>&1; then gunzip stacks_outputs/*.gz; fi
     ]]></command>
 
     <inputs>
@@ -77,11 +79,13 @@
     </inputs>
 
     <outputs>
+        <data format="txt" name="output_log" label="pstacks.log with ${tool.name} on ${on_string}" from_work_dir="pstacks.log" />
+
         <collection name="tabs" type="list" label="Stacks from ${on_string}">
-            <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv" ext="tabular" directory="stacks_outputs" />
-            <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv" ext="tabular" directory="stacks_outputs" />>
-            <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv" ext="tabular" directory="stacks_outputs" />
-            <discover_datasets pattern="(?P&lt;name&gt;.+\.models)\.tsv" ext="tabular" directory="stacks_outputs" />
+            <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
+            <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />>
+            <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
+            <discover_datasets pattern="(?P&lt;name&gt;.+\.models)\.tsv$" ext="tabular" directory="stacks_outputs" />
         </collection>
     </outputs>
 
@@ -90,6 +94,12 @@
             <param name="sample" value="refmap/PopA_01.bam" ftype="bam" />
             <param name="sample_id" value="4" />
 
+            <output name="output_log">
+                <assert_contents>
+                    <has_text text="done." />
+                </assert_contents>
+            </output>
+
             <output_collection name="tabs">
                 <element name="PopA_01.tags">
                     <assert_contents>
diff -r 0f16a6c30085 -r fede8a808d36 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jun 15 06:23:05 2016 -0400
+++ b/tool_dependencies.xml	Sat Jun 25 17:27:31 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" />