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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 57b50253f326baf18bfbf417d8c788b4f5ba66e6
author iuc
date Mon, 27 Jun 2022 18:18:05 +0000
parents 56781a718729
children
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d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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1 <?xml version="1.0"?>
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2 <macros>
1
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3 <token name="@TOOL_VERSION@">0.9.1</token>
2
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4 <token name="@VERSION_SUFFIX@">1</token>
0
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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>
1
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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>
1
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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>
0
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24 <!-- command -->
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25
2
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26 <token name="@SINGLE_BAM@"><![CDATA[
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27 ln -s '$input' 'input.bam' &&
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28 ln -s '$input.metadata.bam_index' 'input.bam.bai' &&
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29 ]]></token>
0
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30 <token name="@BAM@"><![CDATA[
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31 #for $i, $current in enumerate($input)
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32 ln -s '${current}' 'input_${i}.bam' &&
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33 ln -s '${current.metadata.bam_index}' 'input_${i}.bam.bai' &&
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34 #end for
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35 ]]></token>
2
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36 <!-- fasta needs to be linked, because .fai file is created -->
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37 <token name="@FASTA@"><![CDATA[
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38 ln -s '$generic.genome' genome.fa &&
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39 ]]></token>
0
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40 <token name="@DUMP@"><![CDATA[
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41 #if 'dump' in $oo.out
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42 && test -f 'dump.tsv.gz' && bgzip -d 'dump.tsv.gz' || echo 'No dump file.'
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43 #end if
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44 ]]></token>
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45 <token name="@LOG@"><![CDATA[
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46 #if 'log' in $oo.out
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47 |& tee '$out_log'
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48 #end if
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49 ]]></token>
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50 <token name="@VCF@"><![CDATA[
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51 #if 'vcf' in $oo.out
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52 && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.'
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53 #end if
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54 ]]></token>
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55
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56 <!-- input -->
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57
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58 <xml name="cnoffset" token_default="">
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59 <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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60 </xml>
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61 <xml name="coverage" token_label="">
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62 <param argument="--coverage" type="integer" value="10" label="@LABEL@"/>
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63 </xml>
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64 <xml name="exclude">
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65 <param argument="--exclude" type="data" format="tabular" optional="true" label="Select file with regions to exclude"/>
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66 </xml>
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67 <xml name="genome">
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68 <param argument="--genome" type="data" format="fasta" label="Select genome file"/>
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69 </xml>
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70 <xml name="genoqual">
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71 <param name="genoqual" type="integer" value="5" label="Set minimum mapping quality for genotyping" help="(--geno-qual)"/>
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72 </xml>
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73 <xml name="input" token_format="" token_multiple="false" token_label="">
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74 <param name="input" type="data" format="@FORMAT@" multiple="@MULTIPLE@" label="@LABEL@"/>
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75 </xml>
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76 <xml name="maxreadsep" token_default="">
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77 <param argument="--maxreadsep" type="integer" value="@DEFAULT@" label="Set maximum read separation"/>
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78 </xml>
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79 <xml name="maxsize" token_default="" token_label="">
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80 <param argument="--maxsize" type="integer" value="@DEFAULT@" label="@LABEL@"/>
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81 </xml>
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82 <xml name="minclip">
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83 <param argument="--minclip" type="integer" value="25" label="Set minimum clipping length"/>
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84 </xml>
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85 <xml name="mincliquesize">
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86 <param name="mincliquesize" type="integer" value="2" label="Set minimum paired-end/single-read clique size" help="(--min-clique-size)"/>
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87 </xml>
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88 <xml name="minrefsep" token_default="">
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89 <param argument="--minrefsep" type="integer" value="@DEFAULT@" label="Set minimum reference separation"/>
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90 </xml>
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91 <xml name="minsize" token_default="" token_label="">
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92 <param argument="--minsize" type="integer" value="@DEFAULT@" label="@LABEL@"/>
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93 </xml>
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94 <xml name="pass">
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95 <param argument="--pass" type="boolean" truevalue="--pass" falsevalue="" label="Filter sites for PASS?"/>
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96 </xml>
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97 <xml name="ploidy">
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98 <param argument="--ploidy" type="integer" value="2" label="Set baseline ploidy"/>
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99 </xml>
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100 <xml name="samples">
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101 <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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102 </xml>
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103 <xml name="svtype">
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104 <param argument="--svtype" type="select" label="Select type(s) of structural variants to detect">
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105 <option value="ALL" selected="true">All types (ALL)</option>
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106 <option value="DEL">Deletion (DEL)</option>
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107 <option value="DUP">Duplication (DUP)</option>
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108 <option value="INS">Insertion (INS)</option>
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109 <option value="INV">Inversion (INV)</option>
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110 <option value="BND">Translocation (BND)</option>
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111 </param>
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112 </xml>
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113 <xml name="vcffile">
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114 <param argument="--vcffile" type="data" format="bcf,vcf" optional="true" label="Select genotyping file"/>
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115 </xml>
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116
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117 <!-- output -->
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118
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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119 <xml name="bcf">
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120 <data name="out_bcf" format="bcf" from_work_dir="result.bcf" label="${tool.name} on ${on_string}: Result (BCF)">
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121 <filter>'bcf' in oo['out']</filter>
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122 </data>
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123 </xml>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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124 <xml name="vcf">
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125 <data name="out_vcf" format="vcf" from_work_dir="result.vcf" label="${tool.name} on ${on_string}: Result (VCF)">
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126 <filter>'vcf' in oo['out']</filter>
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127 </data>
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128 </xml>
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129 <xml name="dump">
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130 <data name="out_dump" format="tabular" from_work_dir="dump.tsv" label="${tool.name} on ${on_string}: SV-reads">
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131 <filter>'dump' in oo['out']</filter>
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132 </data>
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133 </xml>
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134 <xml name="log">
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135 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
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136 <filter>'log' in oo['out']</filter>
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137 </data>
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138 </xml>
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139
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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140 <!-- help -->
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141
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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142 <token name="@WID@"><![CDATA[
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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143 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.
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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144
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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145 Short-read SV calling
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146
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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147 - *call* to discover and genotype structural variants
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148 - *merge* structural variants across VCF/BCF files and within a single VCF/BCF file
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149 - *filter* somatic or germline structural variants
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150
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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151 Long-read SV calling
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152
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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153 - *lr* for long-read SV discovery
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154
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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155 Copy-number variant calling
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156
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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157 - *cnv* to discover and genotype copy-number variants
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158 - *classify* somatic or germline copy-number variants
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159 ]]></token>
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160 <token name="@REFERENCES@"><![CDATA[
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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161 More information are available on `GitHub <https://github.com/dellytools/delly>`_.
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162 ]]></token>
1
56781a718729 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d76130cdcb21f0390b4e68e733d38575fd5cc6c7"
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163 </macros>