diff samtools_split.xml @ 1:76449db9ee44 draft

planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

--- a/samtools_split.xml	Fri Oct 24 16:22:16 2014 -0400
+++ b/samtools_split.xml	Tue Oct 13 12:56:13 2015 -0400
@@ -1,9 +1,11 @@
-<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>
+<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 $header:
@@ -13,11 +15,8 @@
         #end if
         "${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="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>
@@ -38,16 +37,11 @@
     <help>
 **What it does**
 
-This tool runs the ``samtools split`` command in the SAMtools toolkit.
-
-Split BAM files by read group.
-
-**Citation**
+Splits BAM files on readgroups.
 
-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;`_
-
+This tool is based on ``samtools split`` command. It will generate multiple output datasets for each redagroup from the input dataset. 
 
-If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
     </help>
+    <expand macro="citations"></expand>
 </tool>