Mercurial > repos > iuc > delly_merge

annotate macros.xml @ 1:97c7441aed0d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
author iuc
date Thu, 29 Oct 2020 20:51:37 +0000
parents 6331d804f983
children 148389992630
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6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
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1 <?xml version="1.0"?>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
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2 <macros>
1
97c7441aed0d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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3 <token name="@TOOL_VERSION@">0.8.5</token>
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4 <token name="@VERSION_SUFFIX@">0</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>
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8 <requirement type="package" version="1.10.2">bcftools</requirement>
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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>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
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13 </xml>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
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14 <xml name="citations">
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
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15 <citations>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
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16 <citation type="doi">10.1093/bioinformatics/bts378</citation>
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17 </citations>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
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18 </xml>
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19
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
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20 <!--
1
97c7441aed0d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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21 command
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22 -->
97c7441aed0d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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23
97c7441aed0d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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24 <token name="@BAM@"><![CDATA[
97c7441aed0d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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25 #for $i, $current in enumerate($samples)
97c7441aed0d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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26 ln -s '${current}' 'sample_${i}.bam' &&
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27 ln -s '${current.metadata.bam_index}' 'sample_${i}.bam.bai' &&
97c7441aed0d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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28 #end for
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29 ]]></token>
97c7441aed0d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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30 <token name="@DUMP@"><![CDATA[
97c7441aed0d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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31 #if 'dump' in $oo.out
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32 && test -f 'dump.tsv.gz' && bgzip -d 'dump.tsv.gz' || echo 'No dump file.'
97c7441aed0d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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33 #end if
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34 ]]></token>
97c7441aed0d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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35 <token name="@LOG@"><![CDATA[
97c7441aed0d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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36 #if 'log' in $oo.out
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37 |& tee '$out_log'
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38 #end if
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39 ]]></token>
97c7441aed0d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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40 <token name="@VCF@"><![CDATA[
97c7441aed0d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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41 #if 'vcf' in $oo.out
97c7441aed0d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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42 && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.'
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43 #end if
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44 ]]></token>
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45
97c7441aed0d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
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46 <!--
0
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
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47 input
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48 -->
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49
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
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50 <xml name="exclude">
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51 <param argument="--exclude" type="data" format="tabular" optional="true" label="Select file with regions to exclude"/>
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52 </xml>
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53 <xml name="genome">
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54 <param argument="--genome" type="data" format="fasta" label="Select genome"/>
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55 </xml>
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56 <xml name="genoqual">
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57 <param name="genoqual" type="integer" value="5" label="Set minimum mapping quality for genotyping" help="(--geno-qual)"/>
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58 </xml>
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59 <xml name="minclip">
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60 <param argument="--minclip" type="integer" value="25" label="Set minimum clipping length"/>
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61 </xml>
1
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62 <xml name="maxreadsep" token_default="40">
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63 <param argument="--maxreadsep" type="integer" value="@DEFAULT@" label="Set maximum read separation"/>
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64 </xml>
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65 <xml name="maxsize" token_default="1000000">
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66 <param argument="--maxsize" type="integer" value="@DEFAULT@" label="Set maximum SV size"/>
0
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67 </xml>
1
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68 <xml name="mincliquesize">
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69 <param name="mincliquesize" type="integer" value="2" label="Set minimum min. PE/SR clique size" help="(--min-clique-size)"/>
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70 </xml>
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71 <xml name="minrefsep" token_default="25">
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72 <param argument="--minrefsep" type="integer" value="@DEFAULT@" label="Set minimum reference separation"/>
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73 </xml>
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74 <xml name="minsize">
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75 <param argument="--minsize" type="integer" value="0" label="Set minimum SV size"/>
0
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76 </xml>
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77 <xml name="samples" token_format="bam" token_multiple="true" token_label="Select sample file(s)">
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78 <param name="samples" type="data" format="@FORMAT@" multiple="@MULTIPLE@" label="@LABEL@"/>
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79 </xml>
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80 <xml name="svtype">
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81 <param argument="--svtype" type="select" label="Select type(s) of structural variants to detect">
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82 <option value="ALL" selected="true">All types (ALL)</option>
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83 <option value="DEL">Deletion (DEL)</option>
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84 <option value="INS">Insertion (INS)</option>
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85 <option value="DUP">Duplication (DUP)</option>
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86 <option value="INV">Inversion (INV)</option>
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87 <option value="BND">Translocation (BND)</option>
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88 </param>
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89 </xml>
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90 <xml name="vcffile">
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91 <param argument="--vcffile" type="data" format="vcf,bcf" optional="true" label="Select genotyping file"/>
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92 </xml>
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93
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94 <!--
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
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95 output
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96 -->
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97
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98 <xml name="vcf">
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99 <data name="out_vcf" format="vcf" from_work_dir="result.vcf" label="${tool.name} on ${on_string}: Result (VCF)">
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100 <filter>'vcf' in oo['out']</filter>
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101 </data>
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102 </xml>
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103 <xml name="bcf">
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104 <data name="out_bcf" format="bcf" from_work_dir="result.bcf" label="${tool.name} on ${on_string}: Result (BCF)">
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105 <filter>'bcf' in oo['out']</filter>
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106 </data>
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107 </xml>
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108 <xml name="dump">
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109 <data name="out_dump" format="tabular" from_work_dir="dump.tsv" label="${tool.name} on ${on_string}: SV-reads">
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110 <filter>'dump' in oo['out']</filter>
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111 </data>
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112 </xml>
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113 <xml name="log">
1
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114 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
0
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115 <filter>'log' in oo['out']</filter>
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116 </data>
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117 </xml>
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118
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119 <!--
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120 Help
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121 -->
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122
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123 <token name="@WID@"><![CDATA[
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124 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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125 ]]></token>
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126 <token name="@REFERENCES@"><![CDATA[
1
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127 More information are available on `GitHub <https://github.com/dellytools/delly>`_.
0
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128 ]]></token>
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129 </macros>