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annotate varscan_somatic.xml @ 0:72b8ce355fae 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 13:35:40 -0400
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72b8ce355fae planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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1 <tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.0">
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2 <description>Call germline/somatic variants 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" />
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7 <expand macro="stdio" />
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8 <command><![CDATA[
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9 varscan somatic
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10 '${normal_pileup}'
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11 '${tumor_pileup}'
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12 galaxy_out
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13 --min-coverage ${min_coverage}
72b8ce355fae planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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14 --min-reads2 ${min_reads2}
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15 --min-avg-qual ${min_avg_qual}
72b8ce355fae planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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16 --min-var-freq ${min_var_freq}
72b8ce355fae planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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17 --min-freq-for-hom ${min_freq_for_hom}
72b8ce355fae planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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18 --normal-purity ${normal_purity}
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19 --tumor-purity ${tumor_purity}
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20 --tumor-purity ${tumor_purity}
72b8ce355fae planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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21 --min-coverage-normal ${min_coverage_normal}
72b8ce355fae planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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22 --somatic-p-value ${somatic_p_value}
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23 --p-value ${p_value}
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24 #if str($strand_filter) == 'yes':
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25 --strand-filter 1
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26 #end if
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27
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28 --output-vcf 1
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29 ]]></command>
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30
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31 <inputs>
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32 <param name="normal_pileup" format="pileup" type="data" label="Samtools pileup dataset" help=""/>
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33 <param name="tumor_pileup" format="pileup" type="data" label="Samtools pileup dataset" help=""/>
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34
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35 <expand macro="min_coverage" />
72b8ce355fae planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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36 <param argument="--min-coverage-normal" name="min_coverage_normal" type="integer" value="8" min="1" max="200"
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37 label="Minimum read depth from the normal sample" help="Minimum depth at a position to make a call" />
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38 <param argument="--min-coverage-tumor" name="min_coverage_tumor" type="integer" value="6" min="1" max="200"
72b8ce355fae planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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39 label="Minimum read depth from the tumor sample" help="Minimum depth at a position to make a call" />
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40 <expand macro="min_reads2" />
72b8ce355fae planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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41 <expand macro="min_avg_qual" />
72b8ce355fae planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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42 <expand macro="min_var_freq" value="0.10" />
72b8ce355fae planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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43 <expand macro="min_freq_for_hom" />
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44 <param argument="--normal-purity" name="normal_purity" type="float" value="1.00" min="0" max="1.00"
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45 label="Estimated purity (non-tumor content) of normal sample"/>
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46 <param argument="--tumor-purity" name="tumor_purity" type="float" value="1.00" min="0" max="1.00"
72b8ce355fae planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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47 label="Estimated purity (tumor content) of tumor sample"/>
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48 <expand macro="p_value" label="P-value threshold to call a heterozygote" value="0.99"/>
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49 <param argument="--somatic-p-value" name="somatic_p_value" type="float" value="0.05" min="0" max="1"
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50 label="p-value threshold for calling somatic sites"/>
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51 <expand macro="strand_filter" />
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52 </inputs>
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53 <outputs>
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54 <data name="output_indel" from_work_dir="galaxy_out.indel.vcf" format="vcf"/>
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55 <data name="output_snp" from_work_dir="galaxy_out.snp.vcf" format="vcf"/>
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56 </outputs>
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57 <tests>
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58 <test>
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59 <param name="normal_pileup" value="N_Region_Chr1_CDKN2C.pileup.gz" />
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60 <param name="tumor_pileup" value="T_Region_Chr1_CDKN2C.pileup.gz" />
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61 <param name="min_coverage" value="2" />
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62 <param name="min_coverage_normal" value="2" />
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63 <param name="min_coverage_tumor" value="2" />
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64 <param name="min_reads2" value="1" />
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65 <param name="min_avg_qual" value="5" />
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66 <param name="min_var_freq" value="0.01" />
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67 <param name="min_freq_for_hom" value="0.75" />
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68 <param name="normal_purity" value="0.6" />
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69 <param name="tumor_purity" value="0.6" />
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70 <param name="p_value" value="0.99" />
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71 <output name="output_indel" file="varscan_somatic_indel_result1.vcf" lines_diff="0" />
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72 <output name="output_snp" file="varscan_somatic_snp_result1.vcf" lines_diff="0" />
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73 </test>
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74 </tests>
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75
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76 <help>
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77 **VarScan Overview**
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78
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79 VarScan_ performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data.
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80 It calls variants from a mpileup dataset and produces a VCF 4.1. Full documentation is available online_.
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81
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82 This tool calls germline/somatic variants from tumor-normal pileups.
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83
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84 .. _VarScan: http://dkoboldt.github.io/varscan/
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85 .. _online: http://dkoboldt.github.io/varscan/using-varscan.html
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86
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87 **Input**
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88
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89 ::
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90
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91 mpileup file - The SAMtools mpileup files for the normal and tumor tissue
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93
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94 **Output**
72b8ce355fae planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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95
72b8ce355fae planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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96 VarScan produces a VCF 4.1 dataset as output.
72b8ce355fae planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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97
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98
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99 </help>
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100 <expand macro="citations" />
72b8ce355fae planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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101 </tool>