Mercurial > repos > matt-shirley > sam_dump

changeset 3:0031b2d2e80b draft default tip

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Deleted selected files
author matt-shirley
date Tue, 27 Nov 2012 13:38:25 -0500
parents 39dab3a4578b
children
files sam_dump.xml
diffstat 1 files changed, 0 insertions(+), 33 deletions(-) [+]
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--- a/sam_dump.xml	Wed Nov 14 16:55:35 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,33 +0,0 @@
-<tool id="sam_dump" name="Extract SAM" version="1.0.0">
-  <description> format reads from NCBI SRA.</description>
-  <command>sam-dump $header $aligned $primary '$input' > $output</command>
-  <version_string>sam-dump --version</version_string>
-  <inputs>
-    <param format="sra" name="input" type="data" label="sra archive"/>
-    <param format="text" name="header" type="select" value="">
-      <label>Output SAM header</label>
-      <option value="--header">Yes</option>
-      <option value="--no-header">No</option>
-    </param>
-    <param format="text" name="aligned" type="select" value="">
-      <label>Output unaligned reads</label>
-      <option value="">No</option>
-      <option value="--unaligned">Yes</option>
-    </param>
-    <param format="text" name="primary" type="select" value="">
-      <label>Output only primary aligments</label>
-      <option value="">No</option>
-      <option value="--primary">Yes</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data format="sam" name="output"/>
-  </outputs>
-  <requirements>
-    <requirement type="binary">sam-dump</requirement>
-  </requirements>
-  <help>
-    This tool extracts SAM format reads from SRA archives using sam-dump. The sam-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
-Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
-  </help>
-</tool>