diff STACKS_clone_filter.xml @ 0:42e64fbf4609 draft

planemo upload commit 60a090d1dc89c2eb383feeb35cd6078b9130e0e5-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/STACKS_clone_filter.xml	Tue Feb 02 21:15:50 2016 -0500
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+<tool id="STACKS_clone_filter" name="STACKS: clone_filter" version="0.9.0">
+  <description>Run the STACKS clone_filter program</description>
+
+
+<requirements>
+    <requirement type="package" version="1.18">stacks</requirement>
+</requirements>
+
+<stdio>
+   <exit_code range="1" level="fatal" description="Error in Stacks clone_filter" />
+</stdio>
+
+<command interpreter="python">
+STACKS_clone_filter.py
+#if $data_type.dt_select == 'single':
+  -f $data_type.fname
+#else
+  -1 $data_type.fwd
+  -2 $data_type.rev
+#end if
+</command>
+
+<inputs>
+    <conditional name="data_type">
+      <param name="dt_select" type="select" label="Single or Paired-end">
+          <option value="single">Single</option>
+          <option value="pair">Pair</option>
+      </param>
+      <when value="single">
+          <param name="fname" type="fastq" label="FASTQ" />
+      </when>
+      <when value="pair">
+          <param name="fwd" type="fastq" label="Forward FASTQ" />
+          <param name="rev" type="fastq" label="Reverse FASTQ" />
+      </when>
+  </conditional>
+</inputs>
+
+<outputs>
+    <data format="fastq" name="clean" from_work_dir="job_outputs/clean.fq">
+        <filter>data_type['dt_select'] == 'single' </filter>
+    </data>
+    <data format="fastq" name="clean_fwd" from_work_dir="job_outputs/fwd.fq">
+        <filter>data_type['dt_select'] == 'pair' </filter>
+    </data>
+    <data format="fastq" name="clean_rev" from_work_dir="job_outputs/rev.fq">
+        <filter>data_type['dt_select'] == 'pair' </filter>
+    </data>
+</outputs>
+
+<tests>
+    <test>
+        <param name="dt_select" value="pair" />
+        <param name="fwd" value="fwd.fq" />
+        <param name="rev" value="rev.fq" />
+        <output name="clean_fwd" />
+        <output name="clean_rev" />
+    </test>
+</tests>
+
+<help>
+--------
+
+**Project links:**
+
+`STACKS website &lt;http://creskolab.uoregon.edu/stacks/&gt;`_ .
+
+`STACKS manual &lt;http://creskolab.uoregon.edu/stacks/stacks_manual.pdf&gt;`_ .
+
+`STACKS google group &lt;https://groups.google.com/forum/#!forum/stacks-users&gt;`_ .
+
+</help>
+<citations>
+    <citation type="doi">10.1111/mec.12354</citation>
+    <citation type="doi">10.1111/mec.12330</citation>
+    <citation type="doi">10.1534/g3.111.000240</citation>
+    <citation type="doi">10.1534/genetics.111.127324</citation>
+    <citation type="doi">10.1111/j.1755-0998.2010.02967.x</citation>
+    <citation type="doi">10.1073/pnas.1006538107</citation>
+</citations>
+</tool>