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annotate macros.xml.orig @ 1:148b595025b3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 08:00:10 +0000
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148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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1 <?xml version="1.0"?>
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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2 <macros>
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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3 <token name="@TOOL_VERSION@">0.8.7</token>
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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4 <token name="@VERSION_SUFFIX@">0</token>
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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5 <xml name="requirements">
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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6 <requirements>
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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7 <requirement type="package" version="@TOOL_VERSION@">delly</requirement>
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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8 <requirement type="package" version="1.10.2">bcftools</requirement>
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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9 </requirements>
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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10 </xml>
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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11 <xml name="version_command">
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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12 <version_command><![CDATA[delly -v 2>&1 | grep 'Delly version' | cut -f 3 -d ' ']]></version_command>
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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13 </xml>
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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14 <xml name="citations">
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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15 <citations>
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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16 <citation type="doi">10.1093/bioinformatics/bts378</citation>
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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17 </citations>
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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18 </xml>
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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19 <<<<<<< HEAD
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20
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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21 <!-- command -->
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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22 =======
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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23 <xml name="bio_tools">
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24 <xrefs>
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25 <xref type='bio.tools'>delly2</xref>
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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26 </xrefs>
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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27 </xml>
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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28 <!--
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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29 command
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30 -->
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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31 >>>>>>> 20ed9dd6f (add bio.tools ID)
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32
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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33 <token name="@BAM@"><![CDATA[
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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34 #for $i, $current in enumerate($input)
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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35 ln -s '${current}' 'input_${i}.bam' &&
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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36 ln -s '${current.metadata.bam_index}' 'input_${i}.bam.bai' &&
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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37 #end for
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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38 ]]></token>
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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39 <token name="@DUMP@"><![CDATA[
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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40 #if 'dump' in $oo.out
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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41 && test -f 'dump.tsv.gz' && bgzip -d 'dump.tsv.gz' || echo 'No dump file.'
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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42 #end if
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43 ]]></token>
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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44 <token name="@LOG@"><![CDATA[
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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45 #if 'log' in $oo.out
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46 |& tee '$out_log'
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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47 #end if
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48 ]]></token>
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49 <token name="@VCF@"><![CDATA[
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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50 #if 'vcf' in $oo.out
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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51 && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.'
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52 #end if
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53 ]]></token>
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54
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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55 <!-- input -->
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56
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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57 <xml name="cnoffset" token_default="">
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58 <param name="cnoffset" type="float" min="0.0" max="1.0" value="@DEFAULT@" label="Set minimum CN offset" help="(--cn-offset)"/>
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59 </xml>
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60 <xml name="coverage" token_label="">
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61 <param argument="--coverage" type="integer" value="10" label="@LABEL@"/>
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62 </xml>
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63 <xml name="exclude">
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64 <param argument="--exclude" type="data" format="tabular" optional="true" label="Select file with regions to exclude"/>
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65 </xml>
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66 <xml name="genome">
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67 <param argument="--genome" type="data" format="fasta" label="Select genome file"/>
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68 </xml>
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69 <xml name="genoqual">
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70 <param name="genoqual" type="integer" value="5" label="Set minimum mapping quality for genotyping" help="(--geno-qual)"/>
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71 </xml>
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72 <xml name="input" token_format="" token_multiple="false" token_label="">
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73 <param name="input" type="data" format="@FORMAT@" multiple="@MULTIPLE@" label="@LABEL@"/>
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74 </xml>
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75 <xml name="maxreadsep" token_default="">
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76 <param argument="--maxreadsep" type="integer" value="@DEFAULT@" label="Set maximum read separation"/>
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77 </xml>
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78 <xml name="maxsize" token_default="" token_label="">
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79 <param argument="--maxsize" type="integer" value="@DEFAULT@" label="@LABEL@"/>
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80 </xml>
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81 <xml name="minclip">
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82 <param argument="--minclip" type="integer" value="25" label="Set minimum clipping length"/>
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83 </xml>
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84 <xml name="mincliquesize">
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85 <param name="mincliquesize" type="integer" value="2" label="Set minimum paired-end/single-read clique size" help="(--min-clique-size)"/>
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86 </xml>
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87 <xml name="minrefsep" token_default="">
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88 <param argument="--minrefsep" type="integer" value="@DEFAULT@" label="Set minimum reference separation"/>
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89 </xml>
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90 <xml name="minsize" token_default="" token_label="">
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91 <param argument="--minsize" type="integer" value="@DEFAULT@" label="@LABEL@"/>
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92 </xml>
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93 <xml name="pass">
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94 <param argument="--pass" type="boolean" truevalue="--pass" falsevalue="" label="Filter sites for PASS?"/>
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95 </xml>
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96 <xml name="ploidy">
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97 <param argument="--ploidy" type="integer" value="2" label="Set baseline ploidy"/>
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98 </xml>
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99 <xml name="samples">
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100 <param argument="--samples" type="data" format="tabular" label="Select sample file" help="Two-column sample file listing sample name and tumor or control."/>
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101 </xml>
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102 <xml name="svtype">
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103 <param argument="--svtype" type="select" label="Select type(s) of structural variants to detect">
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104 <option value="ALL" selected="true">All types (ALL)</option>
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105 <option value="DEL">Deletion (DEL)</option>
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106 <option value="DUP">Duplication (DUP)</option>
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107 <option value="INS">Insertion (INS)</option>
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108 <option value="INV">Inversion (INV)</option>
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109 <option value="BND">Translocation (BND)</option>
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110 </param>
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111 </xml>
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112 <xml name="vcffile">
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113 <param argument="--vcffile" type="data" format="bcf,vcf" optional="true" label="Select genotyping file"/>
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114 </xml>
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115
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116 <!-- output -->
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117
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118 <xml name="bcf">
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119 <data name="out_bcf" format="bcf" from_work_dir="result.bcf" label="${tool.name} on ${on_string}: Result (BCF)">
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120 <filter>'bcf' in oo['out']</filter>
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121 </data>
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122 </xml>
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123 <xml name="vcf">
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124 <data name="out_vcf" format="vcf" from_work_dir="result.vcf" label="${tool.name} on ${on_string}: Result (VCF)">
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125 <filter>'vcf' in oo['out']</filter>
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126 </data>
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127 </xml>
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128 <xml name="dump">
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129 <data name="out_dump" format="tabular" from_work_dir="dump.tsv" label="${tool.name} on ${on_string}: SV-reads">
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130 <filter>'dump' in oo['out']</filter>
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131 </data>
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132 </xml>
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133 <xml name="log">
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134 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
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135 <filter>'log' in oo['out']</filter>
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136 </data>
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137 </xml>
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138
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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139 <!-- help -->
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140
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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141 <token name="@WID@"><![CDATA[
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142 Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.
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143
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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144 Short-read SV calling
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145
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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146 - *call* to discover and genotype structural variants
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147 - *merge* structural variants across VCF/BCF files and within a single VCF/BCF file
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148 - *filter* somatic or germline structural variants
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149
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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150 Long-read SV calling
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151
148b595025b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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152 - *lr* for long-read SV discovery
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153
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154 Copy-number variant calling
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155
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156 - *cnv* to discover and genotype copy-number variants
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157 - *classify* somatic or germline copy-number variants
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158 ]]></token>
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159 <token name="@REFERENCES@"><![CDATA[
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160 More information are available on `GitHub <https://github.com/dellytools/delly>`_.
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161 ]]></token>
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162 </macros>