Mercurial > repos > xuebing > sharplab_seq_motif

diff mytools/fastqdump.xml @ 0:39217fa39ff2

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author xuebing
date Tue, 13 Mar 2012 23:34:52 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mytools/fastqdump.xml	Tue Mar 13 23:34:52 2012 -0400
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+<tool id="fastqdump" name="fastq-dump">
+  <description>convert SRA to FASTQ</description>
+  <command>/Users/xuebing/tools/sratoolkit.2.1.9-mac32/fastq-dump -A $input -M $minReadLen -Z > $out_file1 </command>
+  <inputs>
+    <param name="input" format="sra" type="data" label="Original file (SRA)"/>
+    <param name="minReadLen" size="10" type="integer" value="10" label="minimum read length to output"/>
+  </inputs>
+  <outputs>
+    <data format="fastq" name="out_file1" />
+  </outputs>
+  <help>
+
+**What it does**
+
+This is a wrapper of the fastq-dump tool from sra-toolkit. See http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software 
+
+  </help>
+</tool>