Mercurial > repos > iuc > delly_cnv

annotate cnv.xml @ 1:56781a718729 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 19:06:35 +0000
parents d402af96808e
children 8ad49c4272ea
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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>
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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 ## run
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12 delly cnv
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13 ## generic options
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14 --genome '$generic.genome'
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15 --quality '$generic.quality'
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16 --mappability '$generic.mappability'
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17 --ploidy $generic.ploidy
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18 --outfile 'result.bcf'
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19 --covfile 'result.gz'
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20 ## cnv calling options
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21 --sdrd $cnv.sdrd
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22 --cn-offset $cnv.cnoffset
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23 --cnv-size $cnv.cnvsize
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24 #if $cnv.svfile
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25 --svfile $cnv.svfile
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26 #end if
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27 #if $cnv.vcffile
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28 --vcffile '$cnv.vcffile'
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29 #end if
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30 $cnv.segmentation
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31 ## read-depth window options
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32 --window-size $read.windowsize
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33 --window-offset $read.windowoffset
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34 #if $read.bedintervals
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35 --bed-intervals '$read.bedintervals'
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36 #end if
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37 --fraction-window $read.fractionwindow
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38 $read.adaptivewindowing
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39 ## gc fragment normalization options
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40 --scan-window $gc.scanwindow
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41 --fraction-unique $gc.fractionunique
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42 #if $gc.scanregions
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43 --scan-regions '$gc.scanregions'
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44 #end if
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45 --mad-cutoff $gc.madcutoff
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46 --percentile $gc.percentile
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47 $gc.nowindowselection
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48 ## input
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49 '$input'
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50
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51 ## postprocessing
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52 @LOG@
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53 ]]></command>
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54 <inputs>
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55 <expand macro="input" format="bam" label="Select input file"/>
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56 <section name="generic" title="Generic options" expanded="true">
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57 <expand macro="genome"/>
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58 <param argument="--quality" type="integer" value="10" label="Set minimum mapping quality"/>
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59 <param argument="--mappability" type="data" format="fasta" label="Select mappability map file"/>
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60 <param argument="--ploidy" type="integer" value="2" label="Set baseline ploidy"/>
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61 </section>
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62 <section name="cnv" title="CNV calling options" expanded="true">
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63 <param argument="--sdrd" type="integer" value="2" label="Set minimum SD read-depth shift"/>
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64 <expand macro="cnoffset" default="0.1"/>
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65 <param name="cnvsize" type="integer" value="1000" label="Set minimum CNV size" help="(--cnv-size)"/>
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66 <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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67 <expand macro="vcffile"/>
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68 <param argument="--segmentation" type="boolean" truevalue="--segmentation" falsevalue="" label="Use copy-number segmentation?"/>
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69 </section>
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70 <section name="read" title="Read-depth window options" expanded="true">
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71 <param name="windowsize" type="integer" value="10000" label="Set window size" help="(--window-size)"/>
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72 <param name="windowoffset" type="integer" value="10000" label="Set window offset" help="(--window-offset)"/>
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73 <param name="bedintervals" type="data" format="bed" optional="true" label="Select input BED file" help="(--bed-intervals)"/>
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74 <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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75 <param name="adaptivewindowing" type="boolean" truevalue="-a" falsevalue="" label="Use mappable bases for window size?" help="(--adaptive-windowing)"/>
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76 </section>
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77 <section name="gc" title="GC fragment normalization options" expanded="true">
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78 <param name="scanwindow" type="integer" value="10000" label="Set scan window size" help="(--scan-window)"/>
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79 <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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80 <param name="scanregions" type="data" format="bed" optional="true" label="Select file with scanning regions" help="(--scan-regions)"/>
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81 <param name="madcutoff" type="integer" value="3" label="Set count cutoff" help="(median + 3 * mad) (--mad-cutoff)"/>
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82 <param argument="--percentile" type="float" min="0.0" max="1.0" value="0.0005" label="Set threshold for excluding extreme GC fraction"/>
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83 <param name="nowindowselection" type="boolean" truevalue="-n" falsevalue="" label="Skip scan window selection?" help="(--no-window-selection)"/>
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84 </section>
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85 <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"
iuc
parents:
diff changeset
86 <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
parents:
diff changeset
87 <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
parents:
diff changeset
88 <option value="coverage">Coverage</option>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
89 <option value="log">Log</option>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
90 </param>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
91 </section>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
92 </inputs>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
93 <outputs>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
94 <data name="out_cnv" format="bcf" from_work_dir="result.bcf" label="${tool.name} on ${on_string}: CNV">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
95 <filter>'cnv' in oo['out']</filter>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
96 </data>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
97 <data name="out_coverage" format="tabular.gz" from_work_dir="result.gz" label="${tool.name} on ${on_string}: Coverage">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
98 <filter>'coverage' in oo['out']</filter>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
99 </data>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
100 <expand macro="log"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
101 </outputs>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
102 <tests>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
103 <!-- 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"
iuc
parents:
diff changeset
104
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
105 <!-- #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
parents:
diff changeset
106 <test expect_num_outputs="3">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
107 <param name="input" value="normal.bam"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
108 <section name="generic">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
109 <param name="genome" value="genome.fasta"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
110 <param name="mappability" value="map.fasta"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
111 </section>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
112 <section name="oo">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
113 <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
parents:
diff changeset
114 </section>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
115 <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
116 <assert_contents>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
117 <has_size value="0"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
118 </assert_contents>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
119 </output>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
120 <output name="out_coverage">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
121 <assert_contents>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
122 <has_size value="0"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
123 </assert_contents>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
124 </output>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
125 <output name="out_log">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
126 <assert_contents>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
127 <has_text_matching expression=".+Scanning Windows"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
128 <has_line line="***************************************************"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
129 </assert_contents>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
130 </output>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
131 </test>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
132 <!-- #2 -->
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
133 <test expect_num_outputs="3">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
134 <param name="input" value="normal.bam"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
135 <section name="generic">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
136 <param name="genome" value="genome.fasta"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
137 <param name="quality" value="11"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
138 <param name="mappability" value="map.fasta"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
139 <param name="ploidy" value="3"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
140 </section>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
141 <section name="cnv">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
142 <param name="sdrd" value="3"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
143 <param name="cnoffset" value="0.2"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
144 <param name="cnvsize" value="1001"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
145 <param name="segmentation" value="true"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
146 </section>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
147 <section name="read">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
148 <param name="windowsize" value="10001"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
149 <param name="windowoffset" value="9999"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
150 <param name="fractionwindow" value="0.24"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
151 <param name="adaptivewindowing" value="true"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
152 </section>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
153 <section name="gc">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
154 <param name="scanwindow" value="10001"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
155 <param name="fractionunique" value="0.79"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
156 <param name="madcutoff" value="2"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
157 <param name="percentile" value="0.0006"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
158 <param name="nowindowselection" value="true"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
159 </section>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
160 <section name="oo">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
161 <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
parents:
diff changeset
162 </section>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
163 <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
164 <assert_contents>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
165 <has_size value="700" delta="10"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
166 </assert_contents>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
167 </output>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
168 <output name="out_coverage">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
169 <assert_contents>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
170 <has_size value="61"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
171 </assert_contents>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
172 </output>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
173 <output name="out_log">
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
174 <assert_contents>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
175 <has_text_matching expression=".+Done.+"/>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
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176 </assert_contents>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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177 </output>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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178 </test>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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179 </tests>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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180 <help><![CDATA[
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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181 .. class:: infomark
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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182
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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183 **What it does**
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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184
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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185 @WID@
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 **Input**
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 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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190
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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191 **Output**
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 CNV (BCF) and coverage (compressed tabular) files are created.
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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 .. class:: infomark
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 **References**
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 @REFERENCES@
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200 ]]></help>
d402af96808e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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201 <expand macro="citations"/>
1
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202 </tool>