Mercurial > repos > devteam > picard1106
comparison picard_DownsampleSam.xml @ 3:3abc76f7fa12 draft
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| author | devteam |
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| date | Thu, 23 Jan 2014 19:32:48 -0500 |
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| 2:3a18b0c7aa7d | 3:3abc76f7fa12 |
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| 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 <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements> | |
| 4 <command interpreter="python"> | |
| 5 picard_wrapper.py | |
| 6 --input=$inputFile | |
| 7 --output=$outFile | |
| 8 --probability=$probability | |
| 9 --seed=$seed | |
| 10 -j "\$JAVA_JAR_PATH/DownsampleSam.jar" | |
| 11 </command> | |
| 12 <inputs> | |
| 13 <param format="sam" name="inputFile" type="data" label="SAM dataset to be downsampled" | |
| 14 help="If empty, upload or import a SAM dataset." /> | |
| 15 <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" /> | |
| 16 <param name="seed" type="integer" size="5" label="Random seed value" help="(same seed + same probability = same set of reads kept)" value="1" /> | |
| 17 | |
| 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 <!-- Commands: | |
| 26 cp test-data/phiX.fasta . | |
| 27 samtools faidx phiX.fasta | |
| 28 java -jar CreateSequenceDictionary.jar R=phiX.fasta O=phiX.dict URI=phiX.fasta TRUNCATE_NAMES_AT_WHITESPACE=false SPECIES=phiX174 | |
| 29 java -jar ReorderSam.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_RS_input1.bam O=picard_RS_output1.bam REFERENCE=phiX.fasta ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false | |
| 30 --> | |
| 31 <param name="inputFile" value="picard_RS_input1.sam" /> | |
| 32 <param name="probability" value="0.1" /> | |
| 33 <param name="seed" value="2" /> | |
| 34 <output name="outFile" file="picard_RS_output1.sam" ftype="sam" /> | |
| 35 </test> | |
| 36 </tests> | |
| 37 <help> | |
| 38 | |
| 39 .. class:: infomark | |
| 40 | |
| 41 **Purpose** | |
| 42 | |
| 43 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. | |
| 44 | |
| 45 **Picard documentation** | |
| 46 | |
| 47 This is a Galaxy wrapper for DownsampleSam, a part of the external package Picard-tools_. | |
| 48 | |
| 49 .. _Picard-tools: http://www.google.com/search?q=picard+samtools | |
| 50 | |
| 51 ------ | |
| 52 | |
| 53 .. class:: warningmark | |
| 54 | |
| 55 **Warning on SAM/BAM quality** | |
| 56 | |
| 57 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** | |
| 58 flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears | |
| 59 to be the only way to deal with SAM/BAM that cannot be parsed. | |
| 60 | |
| 61 | |
| 62 </help> | |
| 63 </tool> |