# HG changeset patch
# User Matthew Shirley <mdshw5@gmail.com>
# Date 1352757047 18000
# Node ID ba892201bdaddb711fe9d3108852c055f316c887

Wrote a wrapper for NCBI fastq-dump. Initial version.

diff -r 000000000000 -r ba892201bdad fastq_dump.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq_dump.xml	Mon Nov 12 16:50:47 2012 -0500
@@ -0,0 +1,25 @@
+<tool id="fastq_dump" name="Extract fastq from SRA" version="1.0.0">
+  <description>Extract fastq format reads from SRA data archive.</description>
+  <command>fastq-dump --stdout $split $aligned $input > $output </command>
+  <version_string>fastq-dump --version</version_string>
+  <inputs>
+    <param format="sra" name="input" type="data" label="sra archive"/>
+    <param format="text" name="split" type="select" value="">
+      <label>Split read pairs</label>
+      <option value="">No</option>
+      <option value="--split-spot">Yes</option>
+    </param>
+    <param format="text" name="split" type="select" value="">
+      <label>Specify alignment</label>
+      <option value="">All</option>
+      <option value="--aligned">Only aligned</option>
+      <option value="--unaligned">Only unaligned</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="fastqsanger" name="output"/>
+  </outputs>
+  <help>
+    This tool extracts fastqsanger reads from SRA archives using fastq-dump. The fastq-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
+  </help>
+</tool>