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diff fastq_dump.xml @ 0:cdcc400dcafc draft

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Migrated separate tools fastq_dump, sam_dump, and sra_fetch to this repository for further development.
author matt-shirley <mdshw5@gmail.com>
date Tue, 27 Nov 2012 13:31:09 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastq_dump.xml	Tue Nov 27 13:31:09 2012 -0500
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+<tool id="fastq_dump" name="Extract fastq" version="1.0.0">
+  <description> format reads from NCBI SRA.</description>
+  <command>./fastq-dump --log-level fatal --report never --accession '${input.name}' --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="aligned" 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>
+  <stdio>
+    <exit_code range="127" level="fatal" description="Cannot find fastq-dump binary"/>
+  </stdio>
+  <requirements>
+    <requirement type="binary">fastq-dump</requirement>
+  </requirements>
+  <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>