diff barcode_sort.xml @ 0:d838c6a2ec0f draft

planemo upload commit 75d88a8a93e8cd3acb00103bf6a7a07649d17c70

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barcode_sort.xml	Mon Mar 28 18:46:00 2016 -0400
@@ -0,0 +1,55 @@
+<tool id="barcode_sort_stacks" name="Barcode sorting for Stacks"  version="1.0.0" force_history_refresh="True">
+  <description>Run the STACKS populations program</description>
+
+
+<requirements>
+    <requirement type="package" version="5.18">perl</requirement>
+</requirements>
+
+
+
+<stdio>
+   <exit_code range="1" level="fatal" description="Error in script execution" />
+</stdio>
+
+<command interpreter="perl">
+
+barcode_sort.pl $barcode $f1 $f2 $barcoded $nonbarcoded
+
+</command>
+
+<inputs>
+  <param name="barcode" format="txt" type="data" label="Barcode file 1" />
+  <param name="f1" format="fastq" label="First reads" />
+  <param name="f2" format="fastq" label="Second reads" />
+</inputs>
+<outputs>
+  <data format="fastq" name="barcoded" label="Barcoded sequences"/>
+  <data format="fastq" name="nonbarcoded" label="Non barcoded sequences"/>
+</outputs>
+
+<help>
+
+.. class:: infomark
+
+**What it does**
+
+This program takes 2 input sequence files where the barcode can be on either the 1st or 2nd read (but not both) and sorts all barcoded reads into a single file and all non-barcoded files into a second file. This separation is needed for the STACKs program as it does not handle sequences where the barcode is arbitrarily on the 1st or 2nd read.
+
+--------
+
+**Created by:**
+
+Paul Hohenlohe with changes from Brian Hand.
+
+**Integrated by:**
+
+Tiago Antao
+
+
+</help>
+
+<citations>
+</citations>
+</tool>
+