diff stacks_procrad.xml @ 3:11642e18f2b0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393

--- 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>