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1 <tool name="Downsample SAM" id="picard_DownsampleSam" version="1.106.0">
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2 <!-- found on https://bitbucket.org/bwlang/galaxy-dist/src/ca5ded2e18a9ef802c31429e3cb861e8775b24d0/tools/picard/picard_DownsampleSam.xml -->
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3 <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
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4 <command interpreter="python">
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5 picard_wrapper.py
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6 --input=$inputFile
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7 --output=$outFile
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8 --probability=$probability
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9 --seed=$seed
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10 -j "\$JAVA_JAR_PATH/DownsampleSam.jar"
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11 </command>
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12 <inputs>
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13 <param format="sam" name="inputFile" type="data" label="SAM dataset to be downsampled"
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14 help="If empty, upload or import a SAM dataset." />
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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" />
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16 <param name="seed" type="integer" size="5" label="Random seed value" help="(same seed + same probability = same set of reads kept)" value="1" />
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17
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18 </inputs>
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19 <outputs>
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20 <data name="outFile" format="sam" label="${tool.name} on ${on_string}">
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21 </data>
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22 </outputs>
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23 <tests>
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24 <test>
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25 <!-- Commands:
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26 cp test-data/phiX.fasta .
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27 samtools faidx phiX.fasta
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28 java -jar CreateSequenceDictionary.jar R=phiX.fasta O=phiX.dict URI=phiX.fasta TRUNCATE_NAMES_AT_WHITESPACE=false SPECIES=phiX174
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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
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30 -->
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31 <param name="inputFile" value="picard_RS_input1.sam" />
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32 <param name="probability" value="0.1" />
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33 <param name="seed" value="2" />
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34 <output name="outFile" file="picard_RS_output1.sam" ftype="sam" />
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35 </test>
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36 </tests>
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37 <help>
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38
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39 .. class:: infomark
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40
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41 **Purpose**
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42
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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.
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44
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45 **Picard documentation**
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46
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47 This is a Galaxy wrapper for DownsampleSam, a part of the external package Picard-tools_.
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48
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49 .. _Picard-tools: http://www.google.com/search?q=picard+samtools
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50
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51 ------
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52
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53 .. class:: warningmark
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54
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55 **Warning on SAM/BAM quality**
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56
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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**
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58 flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
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59 to be the only way to deal with SAM/BAM that cannot be parsed.
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60
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61
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62 </help>
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63 </tool> |
