# HG changeset patch
# User mdshw5@gmail.com
# Date 1352835398 18000
# Node ID c2995e659548e1761963b3899954876a18484aa6

First version of sam-dump wrapper. Implemented options for filtering output by alignment status and options for output of sam header.

diff -r 000000000000 -r c2995e659548 sam_dump.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sam_dump.xml	Tue Nov 13 14:36:38 2012 -0500
@@ -0,0 +1,30 @@
+<tool id="sam_dump" name="Extract SAM from SRA" version="1.0.0">
+  <description>Extract SAM format reads from SRA data archive.</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>
+  <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>