# HG changeset patch
# User iuc
# Date 1466890115 14400
# Node ID 6a7c5e21873221817a3f88107265394ad57fecbe
# Parent  5bd1418f42278748b59d69020918bc02839f8670
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393

diff -r 5bd1418f4227 -r 6a7c5e218732 macros.xml
--- a/macros.xml	Wed Jun 15 06:24:34 2016 -0400
+++ b/macros.xml	Sat Jun 25 17:28:35 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 5bd1418f4227 -r 6a7c5e218732 stacks_cstacks.xml
--- a/stacks_cstacks.xml	Wed Jun 15 06:24:34 2016 -0400
+++ b/stacks_cstacks.xml	Sat Jun 25 17:28:35 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="stacks_cstacks" name="Stacks: cstacks" version="@WRAPPER_VERSION@.0">
+<tool id="stacks_cstacks" name="Stacks: cstacks" version="@WRAPPER_VERSION@.2">
     <description>build a catalogue of loci</description>
     <macros>
         <import>macros.xml</import>
@@ -14,9 +14,9 @@
 
         #set $samples = ""
         #for $input_file in $input_col:
-            #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" &&
@@ -49,6 +49,8 @@
             #end if
 
             -o stacks_outputs
+
+             > cstacks.log 2>&1
     ]]></command>
 
     <inputs>
@@ -71,6 +73,8 @@
     </inputs>
 
     <outputs>
+        <data format="txt" name="output_log" label="cstacks.log with ${tool.name} on ${on_string}" from_work_dir="cstacks.log" />
+
         <data format="tabular" name="catalogtags" label="Catalog assembled loci (tags) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.tags.tsv" />
         <data format="tabular" name="catalogsnps" label="Catalog model calls (snps) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.snps.tsv" />
         <data format="tabular" name="catalogalleles" label="Catalog haplotypes (alleles) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.alleles.tsv" />
@@ -94,6 +98,12 @@
                </collection>
             </param>
 
+            <output name="output_log">
+                <assert_contents>
+                    <has_text text="done." />
+                </assert_contents>
+            </output>
+
             <!-- catalog -->
             <output name="catalogtags">
                 <assert_contents>
@@ -130,6 +140,12 @@
             </param>
             <param name="gapped|use_gapped" value="true" />
 
+            <output name="output_log">
+                <assert_contents>
+                    <has_text text="done." />
+                </assert_contents>
+            </output>
+
             <!-- catalog -->
             <output name="catalogtags">
                 <assert_contents>
diff -r 5bd1418f4227 -r 6a7c5e218732 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jun 15 06:24:34 2016 -0400
+++ b/tool_dependencies.xml	Sat Jun 25 17:28:35 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" />