Mercurial > repos > iuc > varscan_copynumber

annotate varscan_copynumber.xml @ 0:a584f046e4a7 draft

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planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
author iuc
date Tue, 10 Jul 2018 13:36:24 -0400
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a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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1 <tool id="varscan_copynumber" name="VarScan copynumber" version="@VERSION@.0">
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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2 <description>Determine relative tumor copy number from tumor-normal pileups</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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7 <expand macro="stdio" />
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8 <command><![CDATA[
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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10 varscan copynumber
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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11 '${normal_pileup}'
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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12 '${tumor_pileup}'
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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13 galaxy_out
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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14 --min-coverage ${min_coverage}
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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15 --min-base-qual ${min_base_qual}
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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16 --min-map-qual ${min_map_qual}
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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18 --min-segment-size ${min_segment_size}
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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19 --max-segment-size ${max_segment_size}
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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20 --p-value ${p_value}
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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21 --data-ratio ${data_ratio}
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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23 ]]></command>
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a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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25 <inputs>
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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26 <param name="normal_pileup" format="pileup" type="data" label="Samtools pileup dataset" help=""/>
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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27 <param name="tumor_pileup" format="pileup" type="data" label="Samtools pileup dataset" help=""/>
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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28
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29 <param argument="--min-coverage" name="min_coverage" type="integer" value="20" min="1" max="200"
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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30 label="Minimum read depth" help="Minimum coverage threshold for copynumber segments"/>
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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31
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32 <param argument="--min-base-qual" name="min_base_qual" type="integer" value="20" min="1" max="200"
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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33 label="Minimum base quality to count for coverage"/>
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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34 <param argument="--min-map-qual" name="min_map_qual" type="integer" value="20" min="1" max="200"
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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35 label="Minimum read mapping quality to count for coverage"/>
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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36
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37 <param argument="--min-segment-size" name="min_segment_size" type="integer" value="10" min="1" max="200"
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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38 label="Minimum number of consecutive bases to report a segment" help="" />
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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39 <param argument="--max-segment-size" name="max_segment_size" type="integer" value="100" min="1" max="200"
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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40 label="Max size before a new segment is made" help="" />
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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42 <expand macro="p_value" label="P-value threshold for significant copynumber change-point" value="0.01" />
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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43
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44 <param argument="--data-ratio" name="data_ratio" type="float" value="1.0" min="0.0" max="1.0"
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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45 label="The normal/tumor input data ratio for copynumber adjustment"/>
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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46
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47 <param name="sample_names" type="text" value="" help="Separate sample names by comma; leave blank to use default sample names."/>
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48
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49 </inputs>
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50 <outputs>
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51 <data name="output" from_work_dir="galaxy_out.copynumber" format="interval"/>
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52 </outputs>
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53 <tests>
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54 <test>
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55 <param name="normal_pileup" value="N_Region_Chr1_CDKN2C.pileup.gz" />
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56 <param name="tumor_pileup" value="T_Region_Chr1_CDKN2C.pileup.gz" />
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57 <output name="output" file="varscan_copynumber_result1.interval" lines_diff="0" />
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58 </test>
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59 </tests>
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61 <help>
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62 **VarScan Overview**
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64 VarScan_ performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data.
a584f046e4a7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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65 It calls variants from a mpileup dataset and produces a VCF 4.1. Full documentation is available online_.
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66
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67 This tool estimates the relative tumor copy number from tumor-normal pileups.
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68
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69 .. _VarScan: http://dkoboldt.github.io/varscan/
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70 .. _online: http://dkoboldt.github.io/varscan/using-varscan.html
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72 **Input**
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74 ::
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76 mpileup file - The SAMtools mpileup files for the normal and tumor tissue
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79 **Output**
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81 VarScan produces a VCF 4.1 dataset as output.
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84 </help>
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85 <expand macro="citations" />
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86 </tool>