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comparison picard_DownsampleSam.xml @ 62:876ea92b5c28 draft

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author devteam
date Tue, 18 Feb 2014 16:33:30 -0500
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61:b5063e189f57 62:876ea92b5c28
1 <tool name="Downsample SAM" id="picard_DownsampleSam" version="1.106.0">
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>
4 <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
5 <command interpreter="python">
6 picard_wrapper.py
7 --input=$inputFile
8 --output=$outFile
9 --probability=$probability
10 --seed=$seed
11 -j "\$JAVA_JAR_PATH/DownsampleSam.jar"
12 </command>
13 <inputs>
14 <param format="sam" name="inputFile" type="data" label="SAM dataset to be downsampled"
15 help="If empty, upload or import a SAM 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="seed" type="integer" size="5" label="Random seed value" help="(same seed + same probability = same set of reads kept)" value="1" />
18 </inputs>
19 <outputs>
20 <data name="outFile" format="sam" label="${tool.name} on ${on_string}">
21 </data>
22 </outputs>
23 <tests>
24 <test>
25 <param name="inputFile" value="cleansamtestinput.sam" />
26 <param name="probability" value="0.1" />
27 <param name="seed" value="2" />
28 <output name="outFile" file="downsamplesamoutput.sam" ftype="sam" />
29 </test>
30 </tests>
31 <help>
32
33 .. class:: infomark
34
35 **Purpose**
36
37 Randomly down-sample a SAM or BAM file to retain a random subset of the reads. Mate-pairs are either both kept or both discarded. Reads marked as not primary alignments are all discarded. Each read is given a probability P of being retained - results with the exact same input in the same order and with the same value for RANDOM_SEED will produce the same results.
38
39 **Picard documentation**
40
41 This is a Galaxy wrapper for DownsampleSam, a part of the external package Picard-tools_.
42
43 .. _Picard-tools: http://www.google.com/search?q=picard+samtools
44
45 ------
46
47 .. class:: warningmark
48
49 **Warning on SAM/BAM quality**
50
51 Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
52 flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
53 to be the only way to deal with SAM/BAM that cannot be parsed.
54
55
56 </help>
57 </tool>