Mercurial > repos > devteam > picard1106

comparison picard_SortSam.xml @ 39:70c2d93ea217 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author devteam
date Thu, 13 Feb 2014 21:23:28 -0500
parents
children c810e9bc55af
comparison
equal deleted inserted replaced
38:5042d595e402 39:70c2d93ea217
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 <requirements><requirement type="package">picard</requirement></requirements>
4 <command interpreter="python">
5 picard_wrapper.py
6 --input "$inputFile"
7 -s "$sort_order"
8 -o "$outFile"
9 --output-format $outputFormat
10 -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/SortSam.jar"
11 </command>
12 <inputs>
13 <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to be sorted"
14 help="If empty, upload or import a SAM/BAM dataset." />
15 <param name="sort_order" type="select" label="Sort order">
16 <option value="coordinate" selected="True">coordinate</option>
17 <option value="queryname">queryname</option>
18 <option value="unsorted">unsorted</option>
19 </param>
20 <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" />
21 </inputs>
22 <outputs>
23 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: ${outputFormat}" />
24 <change_format>
25 <when input="outputFormat" value="sam" format="sam" />
26 </change_format>
27 </outputs>
28 <help>
29
30 SortSam
31
32 USAGE: SortSam [options]
33
34 Documentation: http://picard.sourceforge.net/command-line-overview.shtml#SortSam
35
36 Sorts the input SAM or BAM.
37
38 Input and output formats are determined by file extension.
39 Option Description
40 INPUT=File The BAM or SAM file to sort. Required.
41 OUTPUT=File The sorted BAM or SAM output file. Required.
42 SORT_ORDER=SortOrder Sort order of output file Required. Possible values: {unsorted, queryname, coordinate}
43 </help>
44 </tool>
45
46
47
48