Mercurial > repos > devteam > picard1106

comparison picard_DownsampleSam.xml @ 143:b2ca2d181fb4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
fixed downsample sam in picard1106 (accept bam)
author Rayan Chikhi <chikhi@psu.edu>
date Mon, 16 Jun 2014 17:38:15 -0400
parents 876ea92b5c28
children b6662c2c8d64
comparison
equal deleted inserted replaced
142:844fa42ad305 143:b2ca2d181fb4
1 <tool name="Downsample SAM" id="picard_DownsampleSam" version="1.106.0"> 1 <tool name="Downsample SAM/BAM" id="picard_DownsampleSam" version="1.106.0">
2 <!-- found on https://bitbucket.org/bwlang/galaxy-dist/src/ca5ded2e18a9ef802c31429e3cb861e8775b24d0/tools/picard/picard_DownsampleSam.xml --> 2 <!-- found on https://bitbucket.org/bwlang/galaxy-dist/src/ca5ded2e18a9ef802c31429e3cb861e8775b24d0/tools/picard/picard_DownsampleSam.xml -->
3 <description>Down-sample a file to retain a subset of the reads</description> 3 <description>Down-sample a file to retain a subset of the reads</description>
4 <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements> 4 <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
5 <command interpreter="python"> 5 <command interpreter="python">
6 picard_wrapper.py 6 picard_wrapper.py
7 --input=$inputFile 7 --input "$inputFile"
8 --output=$outFile 8 --output "$outFile"
9 --probability=$probability 9 --probability=$probability
10 --output-format $outputFormat
10 --seed=$seed 11 --seed=$seed
11 -j "\$JAVA_JAR_PATH/DownsampleSam.jar" 12 -j "\$JAVA_JAR_PATH/DownsampleSam.jar"
12 </command> 13 </command>
13 <inputs> 14 <inputs>
14 <param format="sam" name="inputFile" type="data" label="SAM dataset to be downsampled" 15 <param format="sam,bam" name="inputFile" type="data" label="SAM/BAM dataset to be downsampled"
15 help="If empty, upload or import a SAM dataset." /> 16 help="If empty, upload or import a SAM or BAM dataset." />
16 <param name="probability" type="float" size="5" label="Probability (between 0 and 1) that any given read will be kept" help="specify 1 to keep all reads, 0.1 to keep 10% of the reads" value="1" /> 17 <param name="probability" type="float" size="5" label="Probability (between 0 and 1) that any given read will be kept" help="specify 1 to keep all reads, 0.1 to keep 10% of the reads" value="1" />
17 <param name="seed" type="integer" size="5" label="Random seed value" help="(same seed + same probability = same set of reads kept)" value="1" /> 18 <param name="seed" type="integer" size="5" label="Random seed value" help="(same seed + same probability = same set of reads kept)" value="1" />
19 <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" />
18 </inputs> 20 </inputs>
19 <outputs> 21 <outputs>
20 <data name="outFile" format="sam" label="${tool.name} on ${on_string}"> 22 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: downsampled ${outputFormat}">
23 <change_format>
24 <when input="outputFormat" value="sam" format="sam" />
25 </change_format>
21 </data> 26 </data>
22 </outputs> 27 </outputs>
28
23 <tests> 29 <tests>
24 <test> 30 <test>
25 <param name="inputFile" value="cleansamtestinput.sam" /> 31 <param name="inputFile" value="cleansamtestinput.sam" ftype="sam" />
26 <param name="probability" value="0.1" /> 32 <param name="probability" value="0.1" />
27 <param name="seed" value="2" /> 33 <param name="seed" value="2" />
34 <param name="outputFormat" value="False" />
28 <output name="outFile" file="downsamplesamoutput.sam" ftype="sam" /> 35 <output name="outFile" file="downsamplesamoutput.sam" ftype="sam" />
29 </test> 36 </test>
30 </tests> 37 </tests>
31 <help> 38 <help>
32 39