# HG changeset patch
# User iuc
# Date 1466890105 14400
# Node ID 344cfdb7dd48245ef7bc64b79912b3c6fcbb05b3
# Parent  e880ddd2d8fa8db4317606feee241ae3502b5e72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393

diff -r e880ddd2d8fa -r 344cfdb7dd48 macros.xml
--- a/macros.xml	Wed Jun 15 06:24:20 2016 -0400
+++ b/macros.xml	Sat Jun 25 17:28:25 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 e880ddd2d8fa -r 344cfdb7dd48 stacks_sstacks.xml
--- a/stacks_sstacks.xml	Wed Jun 15 06:24:20 2016 -0400
+++ b/stacks_sstacks.xml	Sat Jun 25 17:28:25 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="stacks_sstacks" name="Stacks: sstacks" version="@WRAPPER_VERSION@.0">
+<tool id="stacks_sstacks" name="Stacks: sstacks" version="@WRAPPER_VERSION@.1">
     <description>match stacks to a catalog</description>
     <macros>
         <import>macros.xml</import>
@@ -14,9 +14,9 @@
 
         #set $catalog = ""
         #for $input_file in $input_cat:
-            #set $filename = str($input_file.name)
+            #set $filename = str($input_file.element_identifier)
             #if not filename.endswith('.tsv'):
-                #set $filename = ".tsv"
+                #set $filename = $filename + ".tsv"
             #end if
             #if re.search('catalog\.[a-z]+(\.tsv)?$', $filename):
                 ln -s "${input_file}" "stacks_inputs/$filename" &&
@@ -29,9 +29,9 @@
 
         #set $samples = ""
         #for $input_file in $input_tags:
-            #set $filename = str($input_file.name)
+            #set $filename = str($input_file.element_identifier)
             #if not filename.endswith('.tsv'):
-                #set $filename = ".tsv"
+                #set $filename = $filename + ".tsv"
             #end if
             #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename):
                 ln -s "${input_file}" "stacks_inputs/$filename" &&
@@ -60,6 +60,8 @@
             $gapped
 
             -o stacks_outputs
+
+             > sstacks.log 2>&1
     ]]></command>
 
     <inputs>
@@ -74,8 +76,10 @@
     </inputs>
 
     <outputs>
+        <data format="txt" name="output_log" label="sstacks.log with ${tool.name} on ${on_string}" from_work_dir="sstacks.log" />
+
         <collection name="matches" type="list" label="Matches to the catalog on ${on_string}">
-            <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.tsv" ext="tabular" directory="stacks_outputs" />
+            <discover_datasets pattern="(?P&lt;name&gt;.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs" />
         </collection>
     </outputs>
 
@@ -101,6 +105,12 @@
                </collection>
             </param>
 
+            <output name="output_log">
+                <assert_contents>
+                    <has_text text="Outputing to file" />
+                </assert_contents>
+            </output>
+
             <output_collection name="matches">
                 <element name="PopA_01.matches">
                     <assert_contents>
@@ -133,6 +143,12 @@
             <param name="gapped" value="true" />
             <param name="check_haplo" value="true" />
 
+            <output name="output_log">
+                <assert_contents>
+                    <has_text text="Outputing to file" />
+                </assert_contents>
+            </output>
+
             <output_collection name="matches">
                 <element name="PopA_01.matches">
                     <assert_contents>
diff -r e880ddd2d8fa -r 344cfdb7dd48 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jun 15 06:24:20 2016 -0400
+++ b/tool_dependencies.xml	Sat Jun 25 17:28:25 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" />