Mercurial > repos > devteam > picard1106
comparison picard_SortSam.xml @ 67:fda8c1757585 draft
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author | devteam |
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date | Wed, 19 Feb 2014 17:01:18 -0500 |
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66:828b3e80f250 | 67:fda8c1757585 |
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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> | |
47 | |
48 | |
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50 |