diff barcode_sort.xml @ 0:5dc02b8a2a57 draft default tip

planemo upload commit 70654da77972b29181d3b388035836b6fa84d59d-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/barcode_sort.xml	Fri Apr 08 11:38:00 2016 -0400
@@ -0,0 +1,52 @@
+<tool id="barcode_sort_stacks" name="Barcode sorting for Stacks"  version="2.0.2" force_history_refresh="True">
+  <description>Barcode Sorting with Paired-End reads for Stacks</description>
+
+<stdio>
+   <exit_code range="1" level="fatal" description="Error in script execution" />
+</stdio>
+
+<command interpreter="perl">
+
+barcode_sort.pl $barcode $f1 $f2 $barcoded $nonbarcoded true $barcode_length $cut_site $max_errors
+
+</command>
+
+<inputs>
+  <param name="barcode" format="text" type="data" label="Barcode file" />
+  <param name="barcode_length" type="integer" value="6" label="Barcode length" />
+  <param name="f1" type="data" format="fastq" label="First read FASTQ" />
+  <param name="f2" type="data" format="fastq" label="Second read FASTQ" />
+  <param name="cut_site" type="text" value="TGCA" label="Cut site" />
+  <param name="max_errors" type="integer" value="2" label="Maximum number of errors" />
+</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>
+
+</tool>