Mercurial > repos > jbrayet > samtools_1_2_docker

changeset 0:d0472177a68f draft

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Uploaded
author jbrayet
date Wed, 25 Nov 2015 03:21:22 -0500
parents
children 27733b98c415
files bam_to_sam.xml
diffstat 1 files changed, 54 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bam_to_sam.xml	Wed Nov 25 03:21:22 2015 -0500
@@ -0,0 +1,54 @@
+<tool id="bam_to_sam" name="BAM-to-SAM" version="2.0">
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+  <expand macro="version_command"></expand>
+  <expand macro="stdio"></expand>
+  <description>convert BAM to SAM</description>  
+    <command>
+<![CDATA[
+  samtools view -o "${output1}" ${header} "${input1}"
+]]>
+    </command>
+    <inputs>
+        <param format="bam" label="BAM File to Convert" name="input1" type="data" />
+        <param name="header" label="Header options" type="select" help="Allows to choose between seeing the entire dataset with the header, header only, or data only.">
+          <option value="-h">Include header in SAM output (-h)</option>
+          <option value="-H">Print header only (-H)</option>
+          <option value="">Exclude header</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="sam" label="${tool.name} on ${on_string}: converted SAM" name="output1" />
+    </outputs>
+    <tests>
+        <test>
+            <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
+            <param name="header" value="-h" />
+            <output file="bam_to_sam_out1.sam" name="output1" sorted="True" />
+        </test>
+        <test>
+            <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
+            <param name="header" value="-H" />
+            <output file="bam_to_sam_out2.sam" name="output1" sorted="True" />
+        </test>
+        <test>
+            <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
+            <param name="header" value="" />
+            <output file="bam_to_sam_out3.sam" name="output1" sorted="True" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+**What it does**
+
+Converts BAM dataset to SAM using ``samtools view`` command::
+
+ samtools view -o [OUTPUT SAM] [-h|-H] [INPUT BAM] 
+
+]]>
+  </help>
+  <expand macro="citations"></expand>
+</tool>