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1 <tool name="Downsample SAM/BAM" id="picard_DownsampleSam" version="1.126.0">
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2 <description>Downsample a file to retain a subset of the reads</description>
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3 <requirements>
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4 <requirement type="package" version="1.126.0">picard</requirement>
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5 </requirements>
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6
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7 <macros>
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8 <import>picard_macros.xml</import>
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9 </macros>
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10
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11 <command>
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12 @java_options@
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13 java -jar
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14 \$JAVA_JAR_PATH/picard.jar
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15 DownsampleSam
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16 INPUT="${inputFile}"
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17 OUTPUT="${outFile}"
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18 PROBABILITY=${probability}
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19 RANDOM_SEED=${seed}
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20 QUIET=true
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21 VERBOSITY=ERROR
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22 VALIDATION_STRINGENCY=${validation_stringency}
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23 </command>
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24 <inputs>
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25 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM or BAM dataset" />
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26 <param name="probability" type="float" size="4" min="0.0" max="1.0" label="Probability (between 0 and 1) that any given read will be kept" help="PROBABILITY; specify 1 to keep all reads, 0.1 to keep 10% of the reads" value="1" />
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27 <param name="seed" type="integer" size="5" label="Random seed value" help="RANDOM_SEED; default=1" value="1" />
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28
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29 <expand macro="VS" />
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30
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31 </inputs>
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32
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33 <stdio>
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34 <exit_code range="1:" level="fatal"/>
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35 </stdio>
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36
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37 <outputs>
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38 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: downsampled BAM"/>
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39 </outputs>
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40
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41 <tests>
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42 <test>
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43 <param name="inputFile" value="picard_DownsampleSam.bam" ftype="bam" />
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44 <param name="probability" value="0.1" />
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45 <param name="seed" value="1024" />
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46 <param name="validation_stringency" value="LENIENT" />
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47 <output name="outFile" file="picard_DownsampleSam_test1.bam" ftype="bam"/>
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48 </test>
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49 </tests>
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50 <help>
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51
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52 .. class:: infomark
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53
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54 **Purpose**
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55
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56 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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57
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58 @dataset_collections@
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59
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60 @description@
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61
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62 INPUT=File
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63 I=File The input SAM or BAM file to downsample. Required.
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64
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65 OUTPUT=File
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66 O=File The output, downsampled, SAM or BAM file to write. Required.
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67
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68 RANDOM_SEED=Long
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69 R=Long Random seed to use if reproducibilty is desired. Setting to null will cause multiple
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70 invocations to produce different results.
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71
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72 PROBABILITY=Double
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73 P=Double The probability of keeping any individual read, between 0 and 1.
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74
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75
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76
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77 @more_info@
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78 </help>
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79 </tool>
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