Mercurial > repos > drosofff > sam_to_fastq

diff sam_to_fastq.xml @ 0:55107d4a728c draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 0651eb8c86d890e4b223fec82ab3980932710030
author drosofff
date Mon, 21 Mar 2016 17:33:26 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sam_to_fastq.xml	Mon Mar 21 17:33:26 2016 -0400
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+<tool id="sam_to_fastq" name="SAM to FASTQ" version="0.1">
+  <description></description>
+  <command interpreter="python">sam_to_fastq.py --input $input --output $output</command>
+  <inputs>
+       <param name="input" type="data" format="sam" label="SAM file for extraction of aligned reads in FASTQ format"/>
+   </inputs>
+
+ <outputs>
+   <data format="fastqsanger" name="output" label="FASTQ extraction" />
+</outputs>
+
+    <tests>
+        <test>
+            <param ftype="sam" name="input" value="input.sam" />
+            <output file="output.fastq" name="output" />
+        </test>
+    </tests>
+
+
+<help>
+
+**What it does**
+
+Extract sequence and sequence quality of aligned reads in a SAM alignment file and return a FASTQ file containing those reads
+
+</help>
+
+</tool>