Mercurial > repos > iuc > delly_classify

annotate classify.xml @ 0:d3bc6ec7881f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
author iuc
date Fri, 22 Jan 2021 14:33:05 +0000
parents
children d31211a43b19
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0
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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1 <?xml version="1.0"?>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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2 <tool id="delly_classify" name="Delly classify" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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3 <description>somatic or germline copy-number variants</description>
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4 <macros>
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5 <import>macros.xml</import>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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6 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="version_command"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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9 <command detect_errors="exit_code"><![CDATA[
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10 ## initialize
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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11 #if $input.is_of_type('vcf')
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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12 bcftools view -Ob '$input' > 'input.bcf.gz' &&
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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13 bcftools index 'input.bcf.gz' &&
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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14 #else
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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15 ln -s '${input}' 'input.bcf.gz' &&
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16 ln -s '${input.metadata.bcf_index}' 'input.bcf.gz.csi' &&
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17 #end if
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18
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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19 ## run
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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20 delly classify
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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21 ## generic options
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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22 --filter $sv.mode_cond.mode_sel
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23 --outfile 'result.bcf'
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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24 --minsize $generic.minsize
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25 --maxsize $generic.maxsize
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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26 $generic.pass
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27 ## somatic options
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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28 #if $sv.mode_cond.mode_sel == 'somatic'
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29 --samples '$sv.mode_cond.samples'
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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30 --pgerm $sv.mode_cond.pgerm
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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31 --cn-offset $sv.mode_cond.cnoffset
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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32 ## germline options
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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33 #else if $sv.mode_cond.mode_sel == 'germline'
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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34 --ploidy $sv.mode_cond.ploidy
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35 --qual $sv.mode_cond.qual
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36 --maxsd $sv.mode_cond.maxsd
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37 #end if
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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38 ## input
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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39 'input.bcf.gz'
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40
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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41 ## postprocessing
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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42 @LOG@
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43 @VCF@
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44 ]]></command>
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45 <inputs>
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46 <expand macro="input" format="bcf,vcf" label="Select input file"/>
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47 <section name="generic" title="Generic options" expanded="true">
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48 <expand macro="minsize" default="1000" label="Set minimum CNV size"/>
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49 <expand macro="maxsize" default="500000000" label="Set maximum CNV size"/>
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50 <expand macro="pass"/>
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51 </section>
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52 <section name="sv" title="SV calling options" expanded="true">
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53 <conditional name="mode_cond">
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54 <param name="mode_sel" type="select" label="Select filter mode" help="(--filter)">
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55 <option value="somatic" selected="true">Somatic</option>
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56 <option value="germline">Germline</option>
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57 </param>
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58 <when value="somatic">
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59 <expand macro="samples"/>
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60 <param argument="--pgerm" type="float" value="0.05" label="Set probability germline"/>
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61 <expand macro="cnoffset" default="0.2"/>
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62 </when>
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63 <when value="germline">
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64 <expand macro="ploidy"/>
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65 <param argument="--qual" type="integer" value="50" label="Set minimum site quality"/>
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66 <param argument="--maxsd" type="float" value="0.15" label="Set maximum population SD"/>
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67 </when>
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68 </conditional>
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69 </section>
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70 <section name="oo" title="Output options" expanded="true">
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71 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">
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72 <option value="bcf" selected="true">BCF</option>
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73 <option value="log">Log</option>
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74 <option value="vcf">VCF</option>
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75 </param>
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76 </section>
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77 </inputs>
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78 <outputs>
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79 <expand macro="bcf"/>
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80 <expand macro="log"/>
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81 <expand macro="vcf"/>
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82 </outputs>
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83 <tests>
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84 <!-- #1 somatic, default -->
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85 <test expect_num_outputs="3">
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86 <param name="input" value="call_1.bcf.gz"/>
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diff changeset
87 <section name="sv">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
88 <conditional name="mode_cond">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
89 <param name="mode_sel" value="somatic"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
90 <param name="samples" value="samples.tsv"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
91 </conditional>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
92 </section>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
93 <section name="oo">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
94 <param name="out" value="bcf,vcf,log"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
95 </section>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
96 <output name="out_bcf">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
97 <assert_contents>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
98 <has_size value="2322"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
99 </assert_contents>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
100 </output>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
101 <output name="out_log">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
102 <assert_contents>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
103 <has_text_matching expression=".+Done.+"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
104 </assert_contents>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
105 </output>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
106 <output name="out_vcf">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
107 <assert_contents>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
108 <has_size value="7762"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
109 </assert_contents>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
110 </output>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
111 </test>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
112 <!-- #2 somatic -->
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
113 <test expect_num_outputs="3">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
114 <param name="input" value="call_1.bcf.gz"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
115 <section name="generic">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
116 <param name="minsize" value="1001"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
117 <param name="maxsize" value="500000001"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
118 <param name="pass" value="true"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
119 </section>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
120 <section name="sv">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
121 <conditional name="mode_cond">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
122 <param name="mode_sel" value="somatic"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
123 <param name="samples" value="samples.tsv"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
124 <param name="pgerm" value="0.04"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
125 <param name="cnoffset" value="0.19"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
126 </conditional>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
127 </section>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
128 <section name="oo">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
129 <param name="out" value="bcf,vcf,log"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
130 </section>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
131 <output name="out_bcf">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
132 <assert_contents>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
133 <has_size value="2322"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
134 </assert_contents>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
135 </output>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
136 <output name="out_log">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
137 <assert_contents>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
138 <has_text_matching expression=".+Done.+"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
139 </assert_contents>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
140 </output>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
141 <output name="out_vcf">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
142 <assert_contents>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
143 <has_size value="7762"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
144 </assert_contents>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
145 </output>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
146 </test>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
147 <!-- #3 germline, default -->
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
148 <test expect_num_outputs="3">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
149 <param name="input" value="call_1.bcf.gz"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
150 <section name="sv">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
151 <conditional name="mode_cond">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
152 <param name="mode_sel" value="germline"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
153 </conditional>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
154 </section>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
155 <section name="oo">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
156 <param name="out" value="bcf,vcf,log"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
157 </section>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
158 <output name="out_bcf">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
159 <assert_contents>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
160 <has_size value="2270"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
161 </assert_contents>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
162 </output>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
163 <output name="out_log">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
164 <assert_contents>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
165 <has_text_matching expression=".+Done.+"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
166 </assert_contents>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
167 </output>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
168 <output name="out_vcf">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
169 <assert_contents>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
170 <has_size value="7665"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
171 </assert_contents>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
172 </output>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
173 </test>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
174 <!-- #4 germline -->
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
175 <test expect_num_outputs="3">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
176 <param name="input" value="call_1.bcf.gz"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
177 <section name="sv">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents:
diff changeset
178 <conditional name="mode_cond">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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179 <param name="mode_sel" value="germline"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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180 <param name="ploidy" value="1"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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181 <param name="qual" value="51"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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182 <param name="maxsd" value="0.16"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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183 </conditional>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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184 </section>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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185 <section name="oo">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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186 <param name="out" value="bcf,vcf,log"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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187 </section>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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188 <output name="out_bcf">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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189 <assert_contents>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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190 <has_size value="2270"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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191 </assert_contents>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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192 </output>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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193 <output name="out_log">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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194 <assert_contents>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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195 <has_text_matching expression=".+Done.+"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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196 </assert_contents>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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197 </output>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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198 <output name="out_vcf">
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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199 <assert_contents>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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200 <has_size value="7665"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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201 </assert_contents>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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202 </output>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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203 </test>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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204 </tests>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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205 <help><![CDATA[
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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206 .. class:: infomark
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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207
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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208 **What it does**
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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209
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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210 @WID@
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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211
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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212 Delly *classify* for somatic or germline copy-number variants.
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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213
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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214 **Input**
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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215
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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216 Delly *classify* requires an input file in BCF format that can be generated with e.g. Delly *merge*. Additionally a tab-delimited sample description file is required where the first column is the sample id (as in the VCF/BCF file) and the second column is either tumor or control.
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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217
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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218 **Output**
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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219
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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220 The output is available in BCF and VCF format. Additionally a log file is provided.
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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221
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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222 .. class:: infomark
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223
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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224 **References**
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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225
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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226 @REFERENCES@
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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227 ]]></help>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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228 <expand macro="citations"/>
d3bc6ec7881f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
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229 </tool>