diff bam_to_sam.xml @ 0:c9e926d9d87e draft

Uploaded tool tarball with dependencies.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bam_to_sam.xml	Tue Aug 20 09:19:46 2013 -0400
@@ -0,0 +1,66 @@
+<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.3">
+  <requirements>
+    <requirement type="package" version="0.1.18">samtools</requirement>
+  </requirements>
+  <description>converts BAM format to SAM format</description>
+  <command interpreter="python">
+    bam_to_sam.py
+      --input1=$input1
+      --output1=$output1
+      $header
+  </command>
+  <inputs>
+    <param name="input1" type="data" format="bam" label="BAM File to Convert" />
+    <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" label="Include header in output" />
+  </inputs>
+  <outputs>
+    <data format="sam" name="output1" label="${tool.name} on ${on_string}: converted SAM" />
+  </outputs>
+  <tests>
+    <test>
+      <!--
+      Bam-to-Sam command:
+      samtools view -o bam_to_sam_out1.sam test-data/bam_to_sam_in1.bam
+      bam_to_sam_in1.bam can be created from bam_to_sam_in1.sam
+      -->
+      <param name="input1" value="bam_to_sam_in1.bam" ftype="bam" />
+      <param name="header" value="" />
+      <output name="output1" file="bam_to_sam_out1.sam" sorted="True" />
+    </test>
+    <test>
+      <!--
+      Bam-to-Sam command:
+      samtools view -o bam_to_sam_out2.sam test-data/bam_to_sam_in2.bam
+      bam_to_sam_in2.bam can be created from bam_to_sam_in2.sam
+      -->
+      <param name="input1" value="bam_to_sam_in2.bam" ftype="bam" />
+      <param name="header" value="" />
+      <output name="output1" file="bam_to_sam_out2.sam" sorted="True" />
+    </test>
+    <test>
+      <!--
+      Bam-to-Sam command:
+      samtools view -h -o bam_to_sam_out3.sam test-data/bam_to_sam_in1.bam
+      bam_to_sam_in1.bam can be created from bam_to_sam_in1.sam
+      -->
+      <param name="input1" value="bam_to_sam_in1.bam" ftype="bam" />
+      <param name="header" value="--header" />
+      <output name="output1" file="bam_to_sam_out3.sam" sorted="True" lines_diff="6" /><!-- header param not working in func tests so won't produce correct 6-line header (fine in browser) -->
+    </test>
+  </tests>
+  <help>
+
+**What it does**
+
+This tool uses the SAMTools_ toolkit to produce a SAM file from a BAM file.
+
+.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
+
+  </help>
+</tool>