Mercurial > repos > iuc > delly_cnv

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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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1 <?xml version="1.0"?>
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2 <tool id="delly_cnv" name="Delly cnv" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
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3 <description>discover and genotype copy-number variants</description>
1
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4 <expand macro="bio_tools"/>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <expand macro="version_command"/>
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10 <command detect_errors="exit_code"><![CDATA[
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11 @SINGLE_BAM@
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12 @FASTA@
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13 ln -s '$generic.mappability' mappability.fa &&
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14
0
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15 ## run
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16 delly cnv
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17 ## generic options
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18 --genome genome.fa
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19 --quality '$generic.quality'
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20 --mappability mappability.fa
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21 --ploidy $generic.ploidy
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22 --outfile 'result.bcf'
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23 --covfile 'result.gz'
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24 ## cnv calling options
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25 --sdrd $cnv.sdrd
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26 --cn-offset $cnv.cnoffset
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27 --cnv-size $cnv.cnvsize
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28 #if $cnv.svfile
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29 --svfile $cnv.svfile
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30 #end if
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31 #if $cnv.vcffile
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32 --vcffile '$cnv.vcffile'
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33 #end if
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34 $cnv.segmentation
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35 ## read-depth window options
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36 --window-size $read.windowsize
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37 --window-offset $read.windowoffset
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38 #if $read.bedintervals
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39 --bed-intervals '$read.bedintervals'
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40 #end if
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41 --fraction-window $read.fractionwindow
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42 $read.adaptivewindowing
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43 ## gc fragment normalization options
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44 --scan-window $gc.scanwindow
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45 --fraction-unique $gc.fractionunique
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46 #if $gc.scanregions
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47 --scan-regions '$gc.scanregions'
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48 #end if
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49 --mad-cutoff $gc.madcutoff
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50 --percentile $gc.percentile
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51 $gc.nowindowselection
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52 ## input
2
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53 'input.bam'
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54
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55 ## postprocessing
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56 @LOG@
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57 ]]></command>
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58 <inputs>
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59 <expand macro="input" format="bam" label="Select input file"/>
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60 <section name="generic" title="Generic options" expanded="true">
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61 <expand macro="genome"/>
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62 <param argument="--quality" type="integer" value="10" label="Set minimum mapping quality"/>
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63 <param argument="--mappability" type="data" format="fasta" label="Select mappability map file"/>
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64 <param argument="--ploidy" type="integer" value="2" label="Set baseline ploidy"/>
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65 </section>
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66 <section name="cnv" title="CNV calling options" expanded="true">
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67 <param argument="--sdrd" type="integer" value="2" label="Set minimum SD read-depth shift"/>
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68 <expand macro="cnoffset" default="0.1"/>
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69 <param name="cnvsize" type="integer" value="1000" label="Set minimum CNV size" help="(--cnv-size)"/>
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70 <param argument="--svfile" type="data" format="bcf" optional="true" label="Select delly SV file for breakpoint refinement"/> <!-- filetype sv.bcf not supported by galaxy -->
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71 <expand macro="vcffile"/>
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72 <param argument="--segmentation" type="boolean" truevalue="--segmentation" falsevalue="" label="Use copy-number segmentation?"/>
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73 </section>
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74 <section name="read" title="Read-depth window options" expanded="true">
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75 <param name="windowsize" type="integer" value="10000" label="Set window size" help="(--window-size)"/>
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76 <param name="windowoffset" type="integer" value="10000" label="Set window offset" help="(--window-offset)"/>
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77 <param name="bedintervals" type="data" format="bed" optional="true" label="Select input BED file" help="(--bed-intervals)"/>
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78 <param name="fractionwindow" type="float" min="0.0" max="1.0" value="0.25" label="Set minimum callable window fraction" help="(--fraction-window)"/>
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79 <param name="adaptivewindowing" type="boolean" truevalue="-a" falsevalue="" label="Use mappable bases for window size?" help="(--adaptive-windowing)"/>
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80 </section>
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81 <section name="gc" title="GC fragment normalization options" expanded="true">
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82 <param name="scanwindow" type="integer" value="10000" label="Set scan window size" help="(--scan-window)"/>
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83 <param name="fractionunique" type="float" min="0.0" max="1.0" value="0.8" label="Set uniqueness filter for scan windows" help="(--fraction-unique)"/>
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84 <param name="scanregions" type="data" format="bed" optional="true" label="Select file with scanning regions" help="(--scan-regions)"/>
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85 <param name="madcutoff" type="integer" value="3" label="Set count cutoff" help="(median + 3 * mad) (--mad-cutoff)"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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diff changeset
86 <param argument="--percentile" type="float" min="0.0" max="1.0" value="0.0005" label="Set threshold for excluding extreme GC fraction"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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diff changeset
87 <param name="nowindowselection" type="boolean" truevalue="-n" falsevalue="" label="Skip scan window selection?" help="(--no-window-selection)"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
88 </section>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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89 <section name="oo" title="Output options" expanded="true">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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diff changeset
90 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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91 <option value="cnv" selected="true">CNV</option>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
92 <option value="coverage">Coverage</option>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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93 <option value="log">Log</option>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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94 </param>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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95 </section>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
96 </inputs>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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97 <outputs>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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98 <data name="out_cnv" format="bcf" from_work_dir="result.bcf" label="${tool.name} on ${on_string}: CNV">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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99 <filter>'cnv' in oo['out']</filter>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
100 </data>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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101 <data name="out_coverage" format="tabular.gz" from_work_dir="result.gz" label="${tool.name} on ${on_string}: Coverage">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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102 <filter>'coverage' in oo['out']</filter>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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diff changeset
103 </data>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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diff changeset
104 <expand macro="log"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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diff changeset
105 </outputs>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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106 <tests>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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107 <!-- no test implemented for vcffile, svfile, bed-intervals, scanregions -->
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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diff changeset
108
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
109 <!-- #1 default; test data to small, results are empty -->
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
110 <test expect_num_outputs="3">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
111 <param name="input" value="normal.bam"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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112 <section name="generic">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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113 <param name="genome" value="genome.fasta"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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114 <param name="mappability" value="map.fasta"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
115 </section>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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116 <section name="oo">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
117 <param name="out" value="cnv,coverage,log"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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diff changeset
118 </section>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
119 <output name="out_cnv">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
120 <assert_contents>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
121 <has_size value="0"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
122 </assert_contents>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
123 </output>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
124 <output name="out_coverage">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
125 <assert_contents>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
126 <has_size value="0"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
127 </assert_contents>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
128 </output>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
129 <output name="out_log">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
130 <assert_contents>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
131 <has_text_matching expression=".+Scanning Windows"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
132 <has_line line="***************************************************"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
133 </assert_contents>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
134 </output>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
135 </test>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
136 <!-- #2 -->
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
137 <test expect_num_outputs="3">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
138 <param name="input" value="normal.bam"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
139 <section name="generic">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
140 <param name="genome" value="genome.fasta"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
141 <param name="quality" value="11"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
142 <param name="mappability" value="map.fasta"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
143 <param name="ploidy" value="3"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
144 </section>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
145 <section name="cnv">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
146 <param name="sdrd" value="3"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
147 <param name="cnoffset" value="0.2"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
148 <param name="cnvsize" value="1001"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
149 <param name="segmentation" value="true"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
150 </section>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
151 <section name="read">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
152 <param name="windowsize" value="10001"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
153 <param name="windowoffset" value="9999"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
154 <param name="fractionwindow" value="0.24"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
155 <param name="adaptivewindowing" value="true"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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diff changeset
156 </section>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
157 <section name="gc">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
158 <param name="scanwindow" value="10001"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
159 <param name="fractionunique" value="0.79"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
160 <param name="madcutoff" value="2"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
161 <param name="percentile" value="0.0006"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
162 <param name="nowindowselection" value="true"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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diff changeset
163 </section>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
164 <section name="oo">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
165 <param name="out" value="cnv,coverage,log"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
166 </section>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
167 <output name="out_cnv">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
168 <assert_contents>
2
8ad49c4272ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 57b50253f326baf18bfbf417d8c788b4f5ba66e6
iuc
parents: 1
diff changeset
169 <has_size value="645" delta="10"/>
0
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
170 </assert_contents>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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diff changeset
171 </output>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
172 <output name="out_coverage">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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diff changeset
173 <assert_contents>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
174 <has_size value="61"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
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175 </assert_contents>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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176 </output>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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177 <output name="out_log">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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178 <assert_contents>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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179 <has_text_matching expression=".+Done.+"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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180 </assert_contents>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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181 </output>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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182 </test>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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183 </tests>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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184 <help><![CDATA[
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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185 .. class:: infomark
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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186
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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187 **What it does**
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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188
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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189 @WID@
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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190
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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191 **Input**
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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192
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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193 Delly *cnv* requires are a sample (BAM), a genome (FASTA) and a mappability map (FASTA), which is available `here <https://gear.embl.de/data/delly/>`_. Intervals (BED), scanning regions (BED) and a delly SV file for breakpoint refinement (BCF) can be provided optionally.
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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194
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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195 **Output**
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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196
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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197 CNV (BCF) and coverage (compressed tabular) files are created.
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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198
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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199 .. class:: infomark
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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200
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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201 **References**
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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202
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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203 @REFERENCES@
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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204 ]]></help>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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205 <expand macro="citations"/>
1
56781a718729 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d76130cdcb21f0390b4e68e733d38575fd5cc6c7"
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206 </tool>