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annotate picard_DownsampleSam.xml @ 20:2a17c789e0a5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
author iuc
date Tue, 19 Jun 2018 11:28:49 -0400
parents 5053a18d9bc8
children f9242e01365a
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1 <tool name="Downsample SAM/BAM" id="picard_DownsampleSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
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2 <description>Downsample a file to retain a subset of the reads</description>
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3 <macros>
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4 <import>picard_macros.xml</import>
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5 <token name="@WRAPPER_VERSION@">1</token>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 @java_options@
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10 @symlink_element_identifier@
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11 picard
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12 DownsampleSam
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13 INPUT='$escaped_element_identifier'
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14 OUTPUT="${outFile}"
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15 PROBABILITY=${probability}
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16 RANDOM_SEED=${seed}
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17 QUIET=true
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18 VERBOSITY=ERROR
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19 @TMPDIR_OPTION@
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20 VALIDATION_STRINGENCY=${validation_stringency}
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21 ]]></command>
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22 <inputs>
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23 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM or BAM dataset" />
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24 <param name="probability" type="float" min="0.0" max="1.0" label="Probability (between 0 and 1) that any given read will be kept" help="PROBABILITY; specify 1 to keep all reads, 0.1 to keep 10% of the reads" value="1" />
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25 <param name="seed" type="integer" label="Random seed value" help="RANDOM_SEED; default=1" value="1" />
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27 <expand macro="VS" />
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29 </inputs>
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31
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32 <outputs>
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33 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: downsampled BAM"/>
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34 </outputs>
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35
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36 <tests>
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37 <test>
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38 <param name="inputFile" value="picard_DownsampleSam.bam" ftype="bam" />
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39 <param name="probability" value="0.1" />
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40 <param name="seed" value="1024" />
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41 <param name="validation_stringency" value="LENIENT" />
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42 <output name="outFile" file="picard_DownsampleSam_test1.bam" ftype="bam"/>
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43 </test>
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44 </tests>
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45 <help>
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46
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47 .. class:: infomark
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48
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49 **Purpose**
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50
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51 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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52
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53 @dataset_collections@
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54
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55 @description@
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56
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57 INPUT=File
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58 I=File The input SAM or BAM file to downsample. Required.
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59
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60 OUTPUT=File
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61 O=File The output, downsampled, SAM or BAM file to write. Required.
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63 RANDOM_SEED=Long
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64 R=Long Random seed to use if reproducibilty is desired. Setting to null will cause multiple
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65 invocations to produce different results.
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66
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67 PROBABILITY=Double
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68 P=Double The probability of keeping any individual read, between 0 and 1.
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72 @more_info@
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73 </help>
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74 <expand macro="citations" />
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75 </tool>