Mercurial > repos > janislaw > fastqdump

changeset 1:4c5d50211c3d draft default tip

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Uploaded
author janislaw
date Tue, 15 May 2012 10:40:31 -0400
parents 6fe8288d4337
children
files fastqdump.xml
diffstat 1 files changed, 18 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastqdump.xml	Tue May 15 10:40:31 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>