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comparison picard_SortSam.xml @ 67:fda8c1757585 draft

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author devteam
date Wed, 19 Feb 2014 17:01:18 -0500
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66:828b3e80f250 67:fda8c1757585
1 <tool name="Sort Sam" id="picard_SortSam" version="1.106.0">
2 <!-- adapted from https://github.com/najoshi/ucd-biocore-galaxy/blob/master/tools/picard/picard_SortSam.xml -->
3 <!-- warning: the sam format output doesn't work. TODO: fix it -->
4 <description>Sorts SAM or BAM file</description>
5 <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
6 <command interpreter="python">
7 picard_wrapper.py
8 --input "$inputFile"
9 -s "$sort_order"
10 -o "$outFile"
11 --output-format $outputFormat
12 -j "\$JAVA_JAR_PATH/SortSam.jar"
13 </command>
14 <inputs>
15 <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to be sorted"
16 help="If empty, upload or import a SAM/BAM dataset." />
17 <param name="sort_order" type="select" label="Sort order">
18 <option value="coordinate" selected="True">coordinate</option>
19 <option value="queryname">queryname</option>
20 <option value="unsorted">unsorted</option>
21 </param>
22 <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" />
23 </inputs>
24 <outputs>
25 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: ${outputFormat}" />
26 <change_format>
27 <when input="outputFormat" value="sam" format="sam" />
28 </change_format>
29 </outputs>
30 <help>
31
32 SortSam
33
34 USAGE: SortSam [options]
35
36 Documentation: http://picard.sourceforge.net/command-line-overview.shtml#SortSam
37
38 Sorts the input SAM or BAM.
39
40 Input and output formats are determined by file extension.
41 Option Description
42 INPUT=File The BAM or SAM file to sort. Required.
43 OUTPUT=File The sorted BAM or SAM output file. Required.
44 SORT_ORDER=SortOrder Sort order of output file Required. Possible values: {unsorted, queryname, coordinate}
45 </help>
46 </tool>
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