Mercurial > repos > iuc > varscan_somatic

annotate macros.xml @ 9:4e97191a1ff7 draft

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"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156"
author iuc
date Fri, 16 Aug 2019 15:49:54 -0400
parents 2fe9ebb98aad
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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 <macros>
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2 <xml name="requirements">
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3 <requirements>
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4 <requirement type="package" version="@VERSION@">varscan</requirement>
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5 <yield/>
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6 </requirements>
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7 </xml>
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9 <token name="@VERSION@">2.4.3</token>
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11 <xml name="stdio">
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12 <stdio>
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13 <regex match="Exception" source="both" level="fatal" description="Tool exception"/>
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14 <regex match=".*" source="both" level="log" description="tool progress"/>
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15 </stdio>
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16 <version_command><![CDATA[varscan 2>&1 | head -n 1]]></version_command>
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17 </xml>
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19 <xml name="citations">
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20 <citations>
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21 <citation type="doi">10.1101/gr.129684.111</citation>
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22 <citation type="doi">10.1002/0471250953.bi1504s44</citation>
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23 </citations>
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24 </xml>
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25
1
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26 <xml name="input_pileups">
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27 <conditional name="pileup">
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28 <param name="pileup_select" type="select" label="How do you want to provide your pileup files?" help="">
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29 <option value="separated">As separated normal and tumor files</option>
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30 <option value="combined">Normal and Tumor combined in one file</option>
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31 </param>
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32 <when value="separated">
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33 <param name="normal_pileup" format="pileup" type="data" label="Samtools pileup dataset for Normal" help=""/>
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34 <param name="tumor_pileup" format="pileup" type="data" label="Samtools pileup dataset for Tumor" help=""/>
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35 </when>
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36 <when value="combined">
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37 <param name="combined_pileup" format="pileup" type="data" label="Samtools pileup dataset which has combined Normal and Tumor samples" help=""/>
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38 </when>
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39 </conditional>
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40 </xml>
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42 <token name="@INPUT_PILEUPS@">
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43 #if $pileup.pileup_select == 'separated'
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44 '${pileup.normal_pileup}'
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45 '${pileup.tumor_pileup}'
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46 galaxy_out
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47 #else:
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48 '${pileup.combined_pileup}'
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49 galaxy_out
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50 --mpileup 1
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51 #end if
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52
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53 </token>
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54
2
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55 <xml name="min_coverage" token_help="Minimum depth at a position to make a call">
0
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56 <param argument="--min-coverage" name="min_coverage" type="integer" value="8" min="1" max="200"
2
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57 label="Minimum coverage" help="@HELP@"/>
0
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58 </xml>
9
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59 <xml name="min_reads2" token_help="Minimum number (default: 2) of variant-supporting reads at a position required to make a call">
0
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60 <param argument="--min-reads2" name="min_reads2" type="integer" value="2" min="1" max="200"
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61 label="Minimum supporting reads" help="@HELP@"/>
0
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62 </xml>
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63 <xml name="min_avg_qual">
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64 <param argument="--min-avg-qual" name="min_avg_qual" type="integer" value="15" min="1" max="50"
2
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65 label="Minimum base quality"
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66 help="The minimum base quality at the variant position required to use a read for calling" />
0
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67 </xml>
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68 <xml name="min_var_freq" token_value="0.01">
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69 <param argument="--min-var-freq" name="min_var_freq" type="float" value="@VALUE@" min="0" max="1"
2
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70 label="Minimum variant allele frequency"
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71 help="Minimum variant allele frequency (default: @VALUE@) required for calling a variant"/>
0
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72 </xml>
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73 <xml name="min_freq_for_hom">
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74 <param argument="--min-freq-for-hom" name="min_freq_for_hom" type="float" value="0.75" min="0" max="1"
2
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75 label="Minimum homozygous variant allele frequency"
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76 help="Minimum variant allele frequency (default: 0.75) required for calling a homozygous genotype" />
0
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77 </xml>
2
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78 <xml name="p_value" token_value="0.01"
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79 token_label="p-value threshold for calling variants"
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80 token_help="">
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81 <param argument="--p-value" name="p_value" type="float" value="@VALUE@" min="0" max="1"
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82 label="@LABEL@" help="@HELP@"/>
0
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83 </xml>
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84 <xml name="strand_filter">
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85 <param name="strand_filter" type="select" label="Ignore variants with >90% support on one strand">
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86 <option value="no" selected="True">no</option>
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87 <option value="yes">yes</option>
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88 </param>
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89 </xml>
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90
2
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91 <token name="@HELP_HEADER@"><![CDATA[
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92 **VarScan Overview**
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93
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94 VarScan_ performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data. Full documentation of the command line package is available here_.
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95
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96 .. _VarScan: http://dkoboldt.github.io/varscan/
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97 .. _here: http://dkoboldt.github.io/varscan/using-varscan.html
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98 ]]></token>
0
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99 </macros>