changeset 0:5c2a97bb018b draft

Uploaded initial tool definition.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_split.xml	Fri Oct 24 16:22:16 2014 -0400
@@ -0,0 +1,53 @@
+<tool id="samtools_split" name="Split" version="1.0.0">
+    <description>a BAM file by read group</description>
+    <requirements>
+        <requirement type="package" version="1.1">samtools</requirement>
+    </requirements>
+    <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
+    <command><![CDATA[
+        samtools split -f 'Read_Group_%!.bam'
+        #if $header:
+            -u "${output}":"${header}"
+        #else:
+            -u "${output}"
+        #end if
+        "${input_bam}"
+        ]]></command>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Error" />
+    </stdio>
+    <inputs>
+        <param name="input_bam" type="data" format="bam" label="BAM file" multiple="true" />
+        <param name="header" type="data" format="bam,sam" label="Replace header in output file" optional="True" />
+     </inputs>
+    <outputs>
+        <data format="bam" name="output" label="${tool.name} on ${on_string}">
+            <discover_datasets pattern="Read_Group_(?P&lt;designation&gt;.+)\.bam" ext="bam" visible="true" directory="" />
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_bam" value="phiX.bam" ftype="bam" />
+            <output name="output" file="samtools_split_out.bam">
+                <discovered_dataset designation="Mouse" ftype="bam" file="phiX_Mouse.bam" />
+                <discovered_dataset designation="Elephant" ftype="bam" file="phiX_Elephant.bam" />
+                <discovered_dataset designation="Human" ftype="bam" file="phiX_Human.bam" />
+            </output>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+This tool runs the ``samtools split`` command in the SAMtools toolkit.
+
+Split BAM files by read group.
+
+**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;`_
+
+
+If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
+    </help>
+</tool>
+

Binary file test-data/phiX.bam has changed

Binary file test-data/phiX_Elephant.bam has changed

Binary file test-data/phiX_Human.bam has changed

Binary file test-data/phiX_Mouse.bam has changed

Binary file test-data/samtools_split_out.bam has changed

Binary file test-data/tmpV04boNsamtools_split_out.bam has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Oct 24 16:22:16 2014 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="samtools" version="1.1">
+        <repository changeset_revision="c01b111a243b" name="package_samtools_1_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>