Mercurial > repos > iuc > varscan_mpileup

annotate varscan_mpileup.xml @ 0:1e667badbe87 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 13:36:03 -0400
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1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
iuc
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1 <tool id="varscan_mpileup" name="VarScan mpileup" version="@VERSION@.0">
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2 <description>for variant detection</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 ## Set up samples list file.
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10 #if $sample_names.strip() != '':
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11 echo $sample_names | awk -F ',' '{ for (i = 1; i <= NF; i++) { print \$i; } }' > samples_list.txt &&
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12 #end if
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14 ## Set up command + input.
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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15 varscan ${cmd} '${input}'
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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16 --min-coverage ${min_coverage}
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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17 --min-reads2 ${min_reads2}
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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18 --min-avg-qual ${min_avg_qual}
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19 --min-var-freq ${min_var_freq}
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20 --min-freq-for-hom ${min_freq_for_hom}
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21 --p-value ${p_value}
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23 #if str($strand_filter) == 'yes':
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24 --strand-filter 1
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25 #end if
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27 ## Report only variants in consensus.
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28 #if str($cmd) == 'mpileup2cns':
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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29 --variants
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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30 #end if
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32 ## Set up outputs.
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33 --output-vcf 1 > '$output'
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35 #if $sample_names.strip() != '':
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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36 --vcf-sample-list samples_list.txt
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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37 #end if
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39 ]]></command>
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40 <inputs>
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41 <param name="input" format="pileup" type="data" label="Samtools pileup dataset" help=""/>
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42
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43 <param name="cmd" type="select" label="Analysis type">
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44 <option value="mpileup2snp" selected="True">single nucleotide variation</option>
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45 <option value="mpileup2indel">insertions and deletions</option>
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46 <option value="mpileup2cns">consensus genotype</option>
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47 </param>
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48
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49 <expand macro="min_coverage" />
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50 <expand macro="min_reads2" />
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51 <expand macro="min_avg_qual" />
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52 <expand macro="min_var_freq" value="0.01" />
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53 <expand macro="min_freq_for_hom" />
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54 <expand macro="p_value" value="0.99" label="Default p-value threshold for calling variants"/>
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55 <expand macro="strand_filter" />
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56 <param name="sample_names" type="text" value="" help="Separate sample names by comma; leave blank to use default sample names."/>
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57 </inputs>
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58 <outputs>
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59 <data name="output" format="vcf"/>
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60 </outputs>
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61 <tests>
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62 <test>
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63 <param name="input" value="test_in1.pileup" />
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64 <param name="cmd" value="mpileup2cns" />
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65 <param name="min_coverage" value="8" />
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66 <param name="min_reads2" value="2" />
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67 <param name="min_avg_qual" value="15" />
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68 <param name="min_var_freq" value="0.01" />
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69 <param name="min_freq_for_hom" value="0.75" />
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70 <param name="p_value" value="0.99" />
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71 <param name="strand_filter" value="no" />
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72 <param name="sample_names" value="" />
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73 <output name="output" file="varscan_mpileup_result1.vcf" lines_diff="0" />
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74 </test>
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75 </tests>
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76
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77 <help>
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78 **VarScan Overview**
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79
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80 VarScan_ performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data.
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81 It calls variants from a mpileup dataset and produces a VCF 4.1. Full documentation is available online_.
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82
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83 This tool detects variants from pileups.
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84
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85 .. _VarScan: http://dkoboldt.github.io/varscan/
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86 .. _online: http://dkoboldt.github.io/varscan/using-varscan.html
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87
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88 **Input**
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89
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90 ::
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91
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92 mpileup file - The SAMtools mpileup file
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93
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95 **Output**
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96
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97 VarScan produces a VCF 4.1 dataset as output.
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98
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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99 </help>
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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100 <expand macro="citations" />
1e667badbe87 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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101 </tool>