changeset 12:25c5a69f5324 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_split.xml	Wed Nov 25 03:24:01 2015 -0500
@@ -0,0 +1,47 @@
+<tool id="samtools_split" name="Split" version="1.1">
+    <description>BAM dataset on readgroups</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"></expand>
+    <expand macro="stdio"></expand>
+    <expand macro="version_command"></expand>
+    <command><![CDATA[
+        samtools split -f 'Read_Group_%!.bam'
+        #if $header:
+            -u "${output}":"${header}"
+        #else:
+            -u "${output}"
+        #end if
+        "${input_bam}"
+        ]]></command>
+    <inputs>
+        <param name="input_bam" type="data" format="bam" label="BAM file" />
+        <param name="header" type="data" format="bam,sam" label="Replace header in output file" optional="True" />
+     </inputs>
+    <outputs>
+        <data format="bam" name="output" label="${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**
+
+Splits BAM files on readgroups.
+
+This tool is based on ``samtools split`` command. It will generate multiple output datasets for each redagroup from the input dataset. 
+
+    </help>
+    <expand macro="citations"></expand>
+</tool>
+