# HG changeset patch
# User avowinkel
# Date 1435612979 14400
# Node ID 228d0cbc14f902ccd36f2928ff040a63709bc9f7
# Parent  af879fc0d7348099c9c1fbe15ad49492873eabaf
planemo upload for repository https://github.com/kaktus42/galaxytools/tree/master/tools/stacks commit b7d7874d721ed5ac647eecf630b46deaae1a68f2-dirty

diff -r af879fc0d734 -r 228d0cbc14f9 process_radtags.xml
--- a/process_radtags.xml	Fri Jun 26 16:48:45 2015 -0400
+++ b/process_radtags.xml	Mon Jun 29 17:22:59 2015 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="process_radtags" name="process_radtags" version="0.1.0">
+<tool id="process_radtags" name="process_radtags" version="0.1.1">
 
     <description>from Stacks toolbox</description>
 
@@ -146,10 +146,9 @@
         <collection name="split_output" type="list" label="@OUTPUT_NAME_PREFIX@ on ${on_string} (Fastq Collection)">
             <discover_datasets pattern="sample_(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;.+)" directory="splits" />
         </collection>
-        <data format="txt" name="log_file" label="@OUTPUT_NAME_PREFIX@ on ${on_string} (log)">
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.log" ext="txt" directory="output" visible="true" />
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;.+)\.discards" directory="output" visible="true" />
-        </data>
+        <data format="txt" name="log_file" label="@OUTPUT_NAME_PREFIX@ on ${on_string} (log)" />
+        <data format="txt" name="report" label="@OUTPUT_NAME_PREFIX@ on ${on_string} (Report)" from_work_dir="output/process_radtags.log" />
+        <data format_source="fastq_input1" name="discards" label="@OUTPUT_NAME_PREFIX@ on ${on_string} (Discards)" from_work_dir="output/discards.discards" />
     </outputs>
 
     <tests>
@@ -249,4 +248,8 @@
 
 ]]>
     </help>
+
+    <citations>
+        <citation type="doi">10.1111/mec.12354</citation>
+    </citations>
 </tool>
diff -r af879fc0d734 -r 228d0cbc14f9 process_radtags_rename.sh
--- a/process_radtags_rename.sh	Fri Jun 26 16:48:45 2015 -0400
+++ b/process_radtags_rename.sh	Mon Jun 29 17:22:59 2015 -0400
@@ -2,8 +2,7 @@
 
 EXT=$1
 
-mv output/process_radtags.log output/Report.log
-mv output/*.discards output/Discards.${EXT}.discards
+mv output/*.discards output/discards.discards
 mkdir splits
 mv output/sample_* splits
 #ls -lah output splits
diff -r af879fc0d734 -r 228d0cbc14f9 stacks_0.1.1_toolshed.tar.gz
Binary file stacks_0.1.1_toolshed.tar.gz has changed