Mercurial > repos > iuc > delly_call

annotate macros.xml @ 3:6f383714149d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d76130cdcb21f0390b4e68e733d38575fd5cc6c7"
author iuc
date Tue, 14 Dec 2021 19:05:58 +0000
parents 9946bd542898
children c34eab9d5134
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1 <?xml version="1.0"?>
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2 <macros>
3
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3 <token name="@TOOL_VERSION@">0.9.1</token>
1
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4 <token name="@VERSION_SUFFIX@">0</token>
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5 <xml name="requirements">
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">delly</requirement>
3
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8 <requirement type="package" version="1.12">bcftools</requirement>
0
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9 </requirements>
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10 </xml>
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11 <xml name="version_command">
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12 <version_command><![CDATA[delly -v 2>&1 | grep 'Delly version' | cut -f 3 -d ' ']]></version_command>
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13 </xml>
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14 <xml name="citations">
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15 <citations>
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16 <citation type="doi">10.1093/bioinformatics/bts378</citation>
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17 </citations>
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18 </xml>
3
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19 <xml name="bio_tools">
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20 <xrefs>
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21 <xref type="bio.tools">delly2</xref>
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22 </xrefs>
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23 </xml>
2
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24 <!-- command -->
1
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25
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26 <token name="@BAM@"><![CDATA[
2
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27 #for $i, $current in enumerate($input)
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28 ln -s '${current}' 'input_${i}.bam' &&
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29 ln -s '${current.metadata.bam_index}' 'input_${i}.bam.bai' &&
1
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30 #end for
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31 ]]></token>
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32 <token name="@DUMP@"><![CDATA[
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33 #if 'dump' in $oo.out
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34 && test -f 'dump.tsv.gz' && bgzip -d 'dump.tsv.gz' || echo 'No dump file.'
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35 #end if
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36 ]]></token>
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37 <token name="@LOG@"><![CDATA[
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38 #if 'log' in $oo.out
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39 |& tee '$out_log'
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40 #end if
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41 ]]></token>
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42 <token name="@VCF@"><![CDATA[
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43 #if 'vcf' in $oo.out
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44 && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.'
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45 #end if
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46 ]]></token>
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47
2
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48 <!-- input -->
0
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49
2
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50 <xml name="cnoffset" token_default="">
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51 <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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52 </xml>
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53 <xml name="coverage" token_label="">
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54 <param argument="--coverage" type="integer" value="10" label="@LABEL@"/>
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55 </xml>
0
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56 <xml name="exclude">
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57 <param argument="--exclude" type="data" format="tabular" optional="true" label="Select file with regions to exclude"/>
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58 </xml>
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59 <xml name="genome">
2
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60 <param argument="--genome" type="data" format="fasta" label="Select genome file"/>
0
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61 </xml>
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62 <xml name="genoqual">
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63 <param name="genoqual" type="integer" value="5" label="Set minimum mapping quality for genotyping" help="(--geno-qual)"/>
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64 </xml>
2
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65 <xml name="input" token_format="" token_multiple="false" token_label="">
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66 <param name="input" type="data" format="@FORMAT@" multiple="@MULTIPLE@" label="@LABEL@"/>
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67 </xml>
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68 <xml name="maxreadsep" token_default="">
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69 <param argument="--maxreadsep" type="integer" value="@DEFAULT@" label="Set maximum read separation"/>
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70 </xml>
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71 <xml name="maxsize" token_default="" token_label="">
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72 <param argument="--maxsize" type="integer" value="@DEFAULT@" label="@LABEL@"/>
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73 </xml>
0
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74 <xml name="minclip">
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75 <param argument="--minclip" type="integer" value="25" label="Set minimum clipping length"/>
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76 </xml>
2
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77 <xml name="mincliquesize">
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78 <param name="mincliquesize" type="integer" value="2" label="Set minimum paired-end/single-read clique size" help="(--min-clique-size)"/>
1
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79 </xml>
2
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80 <xml name="minrefsep" token_default="">
1
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81 <param argument="--minrefsep" type="integer" value="@DEFAULT@" label="Set minimum reference separation"/>
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82 </xml>
2
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83 <xml name="minsize" token_default="" token_label="">
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84 <param argument="--minsize" type="integer" value="@DEFAULT@" label="@LABEL@"/>
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85 </xml>
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86 <xml name="pass">
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87 <param argument="--pass" type="boolean" truevalue="--pass" falsevalue="" label="Filter sites for PASS?"/>
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88 </xml>
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89 <xml name="ploidy">
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90 <param argument="--ploidy" type="integer" value="2" label="Set baseline ploidy"/>
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91 </xml>
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92 <xml name="samples">
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93 <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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94 </xml>
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95 <xml name="svtype">
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96 <param argument="--svtype" type="select" label="Select type(s) of structural variants to detect">
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97 <option value="ALL" selected="true">All types (ALL)</option>
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98 <option value="DEL">Deletion (DEL)</option>
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99 <option value="DUP">Duplication (DUP)</option>
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100 <option value="INS">Insertion (INS)</option>
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101 <option value="INV">Inversion (INV)</option>
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102 <option value="BND">Translocation (BND)</option>
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103 </param>
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104 </xml>
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105 <xml name="vcffile">
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106 <param argument="--vcffile" type="data" format="bcf,vcf" optional="true" label="Select genotyping file"/>
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107 </xml>
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108
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109 <!-- output -->
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110
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111 <xml name="bcf">
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112 <data name="out_bcf" format="bcf" from_work_dir="result.bcf" label="${tool.name} on ${on_string}: Result (BCF)">
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113 <filter>'bcf' in oo['out']</filter>
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114 </data>
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115 </xml>
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116 <xml name="vcf">
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117 <data name="out_vcf" format="vcf" from_work_dir="result.vcf" label="${tool.name} on ${on_string}: Result (VCF)">
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118 <filter>'vcf' in oo['out']</filter>
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119 </data>
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120 </xml>
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121 <xml name="dump">
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122 <data name="out_dump" format="tabular" from_work_dir="dump.tsv" label="${tool.name} on ${on_string}: SV-reads">
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123 <filter>'dump' in oo['out']</filter>
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124 </data>
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125 </xml>
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126 <xml name="log">
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127 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
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128 <filter>'log' in oo['out']</filter>
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129 </data>
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130 </xml>
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131
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132 <!-- help -->
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133
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134 <token name="@WID@"><![CDATA[
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135 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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136
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137 Short-read SV calling
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138
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139 - *call* to discover and genotype structural variants
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140 - *merge* structural variants across VCF/BCF files and within a single VCF/BCF file
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141 - *filter* somatic or germline structural variants
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142
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143 Long-read SV calling
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144
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145 - *lr* for long-read SV discovery
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146
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147 Copy-number variant calling
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148
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149 - *cnv* to discover and genotype copy-number variants
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150 - *classify* somatic or germline copy-number variants
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151 ]]></token>
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152 <token name="@REFERENCES@"><![CDATA[
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153 More information are available on `GitHub <https://github.com/dellytools/delly>`_.
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154 ]]></token>
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155 </macros>