# HG changeset patch
# User landsj <lands065@umn.edu>
# Date 1371069672 18000
# Node ID 337dc0fe0da1d8e1e7d372e0d6cf2a20580c8d6c
# Parent  d975e466d4435aec9b13106a81f510c610fc2935
add defuse_bamfastq

diff -r d975e466d443 -r 337dc0fe0da1 defuse_bamfastq.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/defuse_bamfastq.xml	Wed Jun 12 15:41:12 2013 -0500
@@ -0,0 +1,65 @@
+<?xml version="1.0"?>
+<tool id="defuse_bamfastq" name="Defuse BamFastq" version="0.6.1">
+  <description>converts a bam file to fastq files.</description>
+  
+  <requirements>
+    <requirement type="package" version="0.6.1">defuse</requirement>
+  </requirements>
+  
+  <version_command>bamfastq --version</version_command>
+
+  <command>bamfastq
+    #if $pair == True :
+      $pair
+    #end if
+
+    #if $multiple == True :
+      $multiple
+    #end if
+
+    #if $rename == True :
+      $rename
+    #end if
+    
+    -2 $fastq2
+    -1 $fastq1
+    -b $bamname
+
+
+  </command>
+
+  <inputs>
+    <param name="bamname" type="data" format="bam" label="Bam filename."/> 
+    <param name="pair" type="boolean" truevalue="-p" falsevalue="" checked="true" label="Name contains pair info as /1 /2."/>
+    <param name="multiple" type="boolean" truevalue="-m" falsevalue="" checked="true" label="Bam contains multiple mappings per read."/>
+    <param name="rename" type="boolean" truevalue="-r" falsevalue="" checked="true" label="Rename with integer IDs."/>
+    
+    
+
+    <stdio>
+      <exit_code range="1:" level="fatal" description="Error" />
+    </stdio>
+
+  </inputs>
+
+  <outputs>
+    <data format="fastqsanger,fastqillumina" name="fastq1" label="fastq1"  />
+    <data format="fastqsanger,fastqillumina" name="fastq2" label="fastq2"  />
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="bamname" ftype="bam" value="tophat_out2h.bam" />
+      <param name="pair" value="True" />
+      <param name="multiple" value="True" />
+      <param name="rename" value="True" />
+      <output name="fastq1" file="testout_defuse1.fq" />
+      <output name="fastq2" file="testout_defuse2.fq" />
+      
+    </test>
+  </tests>
+
+  <help>
+    Turn your dry, flavorless BAM file into delicious fastq files!
+  </help>
+</tool>