Mercurial > repos > iuc > delly_call

annotate macros.xml @ 0:36772204dee5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
author iuc
date Mon, 28 Sep 2020 07:45:21 +0000
parents
children 53d90d86fc83
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36772204dee5 "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"?>
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2 <macros>
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3 <token name="@TOOL_VERSION@">0.8.3</token>
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4 <token name="@DESCRIPTION@"></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>
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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>
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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>
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19
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20 <!--
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21 input
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22 -->
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23
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24 <xml name="exclude">
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25 <param argument="--exclude" type="data" format="tabular" optional="true" label="Select file with regions to exclude"/>
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26 </xml>
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27 <xml name="genome">
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28 <param argument="--genome" type="data" format="fasta" label="Select genome"/>
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29 </xml>
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30 <xml name="genoqual">
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31 <param name="genoqual" type="integer" value="5" label="Set minimum mapping quality for genotyping" help="(--geno-qual)"/>
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32 </xml>
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33 <xml name="minclip">
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34 <param argument="--minclip" type="integer" value="25" label="Set minimum clipping length"/>
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35 </xml>
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36 <xml name="maxreadsep">
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37 <param argument="--maxreadsep" type="integer" value="40" label="Set maximum read separation"/>
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38 </xml>
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39 <xml name="minrefsep">
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40 <param argument="--minrefsep" type="integer" value="25" label="Set minimum reference separation"/>
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41 </xml>
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42 <xml name="samples" token_format="bam" token_multiple="true" token_label="Select sample file(s)">
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43 <param name="samples" type="data" format="@FORMAT@" multiple="@MULTIPLE@" label="@LABEL@"/>
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44 </xml>
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45 <xml name="svtype">
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46 <param argument="--svtype" type="select" label="Select type(s) of structural variants to detect">
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47 <option value="ALL" selected="true">All types (ALL)</option>
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48 <option value="DEL">Deletion (DEL)</option>
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49 <option value="INS">Insertion (INS)</option>
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50 <option value="DUP">Duplication (DUP)</option>
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51 <option value="INV">Inversion (INV)</option>
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52 <option value="BND">Translocation (BND)</option>
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53 </param>
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54 </xml>
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55 <xml name="vcffile">
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56 <param argument="--vcffile" type="data" format="vcf,bcf" optional="true" label="Select genotyping file"/>
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57 </xml>
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58
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59 <!--
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60 output
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61 -->
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62
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63 <xml name="vcf">
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64 <data name="out_vcf" format="vcf" from_work_dir="result.vcf" label="${tool.name} on ${on_string}: Result (VCF)">
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65 <filter>'vcf' in oo['out']</filter>
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66 </data>
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67 </xml>
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68 <xml name="bcf">
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69 <data name="out_bcf" format="bcf" from_work_dir="result.bcf" label="${tool.name} on ${on_string}: Result (BCF)">
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70 <filter>'bcf' in oo['out']</filter>
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71 </data>
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72 </xml>
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73 <xml name="dump">
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74 <data name="out_dump" format="tabular" from_work_dir="dump.tsv" label="${tool.name} on ${on_string}: SV-reads">
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75 <filter>'dump' in oo['out']</filter>
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76 </data>
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77 </xml>
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78 <xml name="log">
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79 <data name="out_log" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: Log">
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80 <filter>'log' in oo['out']</filter>
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81 </data>
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82 </xml>
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83
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84 <!--
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85 Help
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86 -->
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87
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88 <token name="@WID@"><![CDATA[
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89 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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90 ]]></token>
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91 <token name="@REFERENCES@"><![CDATA[
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
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92 More information are available on `github <https://github.com/dellytools/delly>`_.
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
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93 ]]></token>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
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94 </macros>