Mercurial > repos > iuc > varscan_mpileup

annotate varscan_mpileup.xml @ 8:4c69f367c326 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 1232893782204bb041dd6ed46711295cb0bfc03f"
author iuc
date Sat, 04 Dec 2021 22:21:15 +0000
parents 83d72fb136f7
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83d72fb136f7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
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1 <tool id="varscan_mpileup" name="VarScan mpileup" version="@VERSION@.1">
0
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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2 <description>for variant detection</description>
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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3 <macros>
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4 <import>macros.xml</import>
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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5 </macros>
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83d72fb136f7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
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6 <expand macro="requirements">
83d72fb136f7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
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7 <requirement type="package" version="4.2.1">gawk</requirement>
83d72fb136f7 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919
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8 </expand>
0
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9 <expand macro="stdio" />
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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10 <command><![CDATA[
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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11 ## Set up samples list file.
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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12 #if $sample_names.strip() != '':
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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13 echo $sample_names | awk -F ',' '{ for (i = 1; i <= NF; i++) { print \$i; } }' > samples_list.txt &&
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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14 #end if
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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16 ## Set up command + input.
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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17 varscan ${cmd} '${input}'
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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18 --min-coverage ${min_coverage}
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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19 --min-reads2 ${min_reads2}
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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20 --min-avg-qual ${min_avg_qual}
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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21 --min-var-freq ${min_var_freq}
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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22 --min-freq-for-hom ${min_freq_for_hom}
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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23 --p-value ${p_value}
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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25 #if str($strand_filter) == 'yes':
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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26 --strand-filter 1
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27 #end if
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29 ## Report only variants in consensus.
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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30 #if str($cmd) == 'mpileup2cns':
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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31 --variants
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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32 #end if
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33
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34 ## Set up outputs.
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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35 --output-vcf 1 > '$output'
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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37 #if $sample_names.strip() != '':
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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38 --vcf-sample-list samples_list.txt
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39 #end if
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41 ]]></command>
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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42 <inputs>
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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43 <param name="input" format="pileup" type="data" label="Samtools pileup dataset" help=""/>
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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44
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45 <param name="cmd" type="select" label="Analysis type">
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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46 <option value="mpileup2snp" selected="True">single nucleotide variation</option>
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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47 <option value="mpileup2indel">insertions and deletions</option>
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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48 <option value="mpileup2cns">consensus genotype</option>
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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49 </param>
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50
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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51 <expand macro="min_coverage" />
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52 <expand macro="min_reads2" />
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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53 <expand macro="min_avg_qual" />
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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54 <expand macro="min_var_freq" value="0.01" />
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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55 <expand macro="min_freq_for_hom" />
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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56 <expand macro="p_value" value="0.99" label="Default p-value threshold for calling variants"/>
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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57 <expand macro="strand_filter" />
99b46f1473cd planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
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58 <param name="sample_names" type="text" value="" help="Separate sample names by comma; leave blank to use default sample names."/>
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59 </inputs>
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60 <outputs>
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61 <data name="output" format="vcf"/>
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62 </outputs>
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63 <tests>
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64 <test>
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65 <param name="input" value="test_in1.pileup" />
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66 <param name="cmd" value="mpileup2cns" />
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67 <param name="min_coverage" value="8" />
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68 <param name="min_reads2" value="2" />
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69 <param name="min_avg_qual" value="15" />
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70 <param name="min_var_freq" value="0.01" />
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71 <param name="min_freq_for_hom" value="0.75" />
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72 <param name="p_value" value="0.99" />
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73 <param name="strand_filter" value="no" />
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74 <param name="sample_names" value="" />
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75 <output name="output" file="varscan_mpileup_result1.vcf" lines_diff="0" />
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76 </test>
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77 </tests>
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78
2
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79 <help><![CDATA[
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80 @HELP_HEADER@
0
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81
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82 **Input**
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83
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84 ::
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86 mpileup file - The SAMtools mpileup file
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87
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88
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89 **Output**
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90
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91 VarScan produces a VCF 4.1 dataset as output.
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92
2
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93 ]]></help>
0
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94 <expand macro="citations" />
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95 </tool>