Mercurial > repos > matt-shirley > fastq_dump

changeset 6:7a9ddfd55d71 draft default tip

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Deleted selected files
author matt-shirley
date Tue, 27 Nov 2012 13:37:36 -0500
parents 73656a524d45
children
files fastq_dump.xml
diffstat 1 files changed, 0 insertions(+), 31 deletions(-) [+]
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--- a/fastq_dump.xml	Thu Nov 15 10:50:03 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
-<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>