Mercurial > repos > iuc > delly_filter

annotate filter.xml @ 3:d2590fe6793f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d76130cdcb21f0390b4e68e733d38575fd5cc6c7"
author iuc
date Tue, 14 Dec 2021 19:06:53 +0000
parents 6184cfc70e28
children
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1 <?xml version="1.0"?>
1
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2 <tool id="delly_filter" name="Delly filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
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3 <description>somatic or germline structural variants</description>
3
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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 ## initialize
2
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12 #if $input.is_of_type('vcf')
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13 bcftools view -Ob '$input' > 'input.bcf.gz' &&
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14 bcftools index 'input.bcf.gz' &&
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15 #else
2
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16 ln -s '${input}' 'input.bcf.gz' &&
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17 ln -s '${input.metadata.bcf_index}' 'input.bcf.gz.csi' &&
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18 #end if
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19
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20 ## run
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21 delly filter
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22 ## generic options
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23 --filter $sv.mode_cond.mode_sel
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24 --outfile 'result.bcf'
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25 --altaf $generic.altaf
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26 --minsize $generic.minsize
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27 --maxsize $generic.maxsize
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28 --ratiogeno $generic.ratiogeno
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29 $generic.pass
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30 ## somatic options
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31 #if $sv.mode_cond.mode_sel == 'somatic'
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32 --samples '$sv.mode_cond.samples'
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33 --coverage $sv.mode_cond.coverage
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34 --controlcontamination $sv.mode_cond.controlcontamination
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35 ## germline options
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36 #else if $sv.mode_cond.mode_sel == 'germline'
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37 --gq $sv.mode_cond.gq
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38 --rddel $sv.mode_cond.rddel
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39 --rddup $sv.mode_cond.rddup
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40 #end if
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41 ## input
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42 'input.bcf.gz'
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43
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44 ## postprocessing
1
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45 @LOG@
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46 @VCF@
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47 ]]></command>
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48 <inputs>
2
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49 <expand macro="input" format="bcf,vcf" label="Select input file"/>
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50 <section name="generic" title="Generic options" expanded="true">
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51 <param argument="--altaf" type="float" value="0.2" min="0.0" max="1.0" label="Set minimum fractional ALT support"/>
2
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52 <expand macro="minsize" default="0" label="Set minimum SV size"/>
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53 <expand macro="maxsize" default="500000000" label="Set maximum SV size"/>
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54 <param argument="--ratiogeno" type="float" value="0.75" min="0.0" max="1.0" label="Set minimum fraction of genotyped samples"/>
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55 <param argument="--pass" type="boolean" truevalue="--pass" falsevalue="" label="Filter sites for PASS?"/>
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56 </section>
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57 <section name="sv" title="SV calling options" expanded="true">
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58 <conditional name="mode_cond">
2
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59 <param name="mode_sel" type="select" label="Select filter mode" help="(--filter)">
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60 <option value="somatic" selected="true">Somatic</option>
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61 <option value="germline">Germline</option>
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62 </param>
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63 <when value="somatic">
2
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64 <expand macro="samples"/>
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65 <expand macro="coverage" label="Set minimum coverage in tumor"/>
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66 <param argument="--controlcontamination" type="float" value="0.0" min="0.0" max="1.0" label="Set maximum fractional ALT support in control"/>
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67 </when>
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68 <when value="germline">
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69 <param argument="--gq" type="integer" value="15" label="Set minimum median GQ for carriers and non-carriers"/>
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70 <param argument="--rddel" type="float" value="0.8" label="Set maximum read-depth ratio of carrier vs. non-carrier for a deletion"/>
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71 <param argument="--rddup" type="float" value="1.2" label="Set minimum read-depth ratio of carrier vs. non-carrier for a duplication"/>
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72 </when>
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73 </conditional>
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74 </section>
2
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75 <section name="oo" title="Output options" expanded="true">
0
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76 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">
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77 <option value="bcf" selected="true">BCF</option>
2
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78 <option value="log">Log</option>
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79 <option value="vcf">VCF</option>
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80 </param>
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81 </section>
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82 </inputs>
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83 <outputs>
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84 <expand macro="bcf"/>
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85 <expand macro="log"/>
2
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86 <expand macro="vcf"/>
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iuc
parents:
diff changeset
87 </outputs>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
88 <tests>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
89 <!-- #1 default, somatic, bcf -->
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
90 <test expect_num_outputs="2">
2
6184cfc70e28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
91 <param name="input" value="call_1.bcf.gz"/>
0
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
92 <section name="sv">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
93 <conditional name="mode_cond">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
94 <param name="mode_sel" value="somatic"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
95 <param name="samples" value="samples.tsv"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
96 </conditional>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
97 </section>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
98 <section name="oo">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
99 <param name="out" value="vcf,bcf"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
100 </section>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
101 <output name="out_bcf">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
102 <assert_contents>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
103 <has_size value="2281" delta="10"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
104 </assert_contents>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
105 </output>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
106 <output name="out_vcf">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
107 <assert_contents>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
108 <has_n_lines n="140"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
109 <has_line line="##fileformat=VCFv4.2"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
110 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;NORMAL&#009;TUMOR"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
111 </assert_contents>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
112 </output>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
113 </test>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
114 <!-- #2 somatic, bcf -->
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
115 <test expect_num_outputs="3">
2
6184cfc70e28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
116 <param name="input" value="call_1.bcf.gz"/>
0
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
117 <section name="generic">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
118 <param name="altaf" value="0.3"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
119 <param name="minsize" value="1"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
120 <param name="maxsize" value="500000001"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
121 <param name="ratiogeno" value="0.76"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
122 <param name="pass" value="true"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
123 </section>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
124 <section name="sv">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
125 <conditional name="mode_cond">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
126 <param name="mode_sel" value="somatic"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
127 <param name="samples" value="samples.tsv"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
128 <param name="coverage" value="11"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
129 <param name="controlcontamination" value="0.1"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
130 </conditional>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
131 </section>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
132 <section name="oo">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
133 <param name="out" value="vcf,bcf,log"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
134 </section>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
135 <output name="out_bcf">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
136 <assert_contents>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
137 <has_size value="2281" delta="10"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
138 </assert_contents>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
139 </output>
2
6184cfc70e28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
140 <output name="out_log">
6184cfc70e28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
141 <assert_contents>
6184cfc70e28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
142 <has_text_matching expression=".+Done\."/>
6184cfc70e28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
143 </assert_contents>
6184cfc70e28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
144 </output>
0
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
145 <output name="out_vcf">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
146 <assert_contents>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
147 <has_n_lines n="140"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
148 <has_line line="##fileformat=VCFv4.2"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
149 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;NORMAL&#009;TUMOR"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
150 </assert_contents>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
151 </output>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
152 </test>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
153 <!-- #3 default, germline, bcf -->
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
154 <test expect_num_outputs="2">
2
6184cfc70e28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
155 <param name="input" value="call_1.bcf.gz"/>
0
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
156 <section name="sv">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
157 <conditional name="mode_cond">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
158 <param name="mode_sel" value="germline"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
159 </conditional>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
160 </section>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
161 <section name="oo">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
162 <param name="out" value="vcf,bcf"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
163 </section>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
164 <output name="out_bcf">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
165 <assert_contents>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
166 <has_size value="2264" delta="10"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
167 </assert_contents>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
168 </output>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
169 <output name="out_vcf">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
170 <assert_contents>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
171 <has_n_lines n="139"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
172 <has_line line="##fileformat=VCFv4.2"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
173 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;NORMAL&#009;TUMOR"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
174 </assert_contents>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
175 </output>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
176 </test>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
177 <!-- #4 germline, bcf -->
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
178 <test expect_num_outputs="3">
2
6184cfc70e28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
179 <param name="input" value="call_1.bcf.gz"/>
0
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
180 <section name="generic">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
181 <param name="altaf" value="0.1"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
182 <param name="minsize" value="1"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
183 <param name="maxsize" value="500000001"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
184 <param name="ratiogeno" value="0.76"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
185 <param name="pass" value="true"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
186 </section>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
187 <section name="sv">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
188 <conditional name="mode_cond">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
189 <param name="mode_sel" value="germline"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
190 <param name="gq" value="14"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
191 <param name="rddel" value="0.7"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
192 <param name="rddup" value="1.3"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
193 </conditional>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
194 </section>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
195 <section name="oo">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
196 <param name="out" value="vcf,bcf,log"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
197 </section>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
198 <output name="out_bcf">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
199 <assert_contents>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
200 <has_size value="2264" delta="10"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
201 </assert_contents>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
202 </output>
2
6184cfc70e28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
203 <output name="out_log">
6184cfc70e28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
204 <assert_contents>
6184cfc70e28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
205 <has_text_matching expression=".+Done\."/>
6184cfc70e28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
206 </assert_contents>
6184cfc70e28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
207 </output>
0
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
208 <output name="out_vcf">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
209 <assert_contents>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
210 <has_n_lines n="139"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
211 <has_line line="##fileformat=VCFv4.2"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
212 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;NORMAL&#009;TUMOR"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
213 </assert_contents>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
214 </output>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
215 </test>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
216 <!-- #5 default, somatic, vcf -->
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
217 <test expect_num_outputs="2">
2
6184cfc70e28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
218 <param name="input" value="call_1.vcf.gz"/>
0
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
219 <section name="sv">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
220 <conditional name="mode_cond">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
221 <param name="mode_sel" value="somatic"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
222 <param name="samples" value="samples.tsv"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
223 </conditional>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
224 </section>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
225 <section name="oo">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
226 <param name="out" value="vcf,bcf"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
227 </section>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
228 <output name="out_bcf">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
229 <assert_contents>
2
6184cfc70e28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
230 <has_size value="2451" delta="10"/>
0
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
231 </assert_contents>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
232 </output>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
233 <output name="out_vcf">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
234 <assert_contents>
3
d2590fe6793f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d76130cdcb21f0390b4e68e733d38575fd5cc6c7"
iuc
parents: 2
diff changeset
235 <has_n_lines n="143"/>
0
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
236 <has_line line="##fileformat=VCFv4.2"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
237 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;NORMAL&#009;TUMOR"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
238 </assert_contents>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
239 </output>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
240 </test>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
241 </tests>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
242 <help><![CDATA[
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
243 .. class:: infomark
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
244
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
245 **What it does**
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
246
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
247 @WID@
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
248
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
249 **Input**
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
250
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
251 *Somatic* filtering requires a called SV input with at least one tumor sample and a matched control sample. In addition, a tab-delimited sample description needs to be provided, in which the first column holds the sample ids (as found in the VCF/BCF input) and the second column specifies either tumor or control.
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
252
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
253 *Germline* SV calling is done by sample for high-coverage genomes or in small batches for low-coverage genomes.
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
254
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
255 **Output**
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
256
2
6184cfc70e28 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
257 The output is available in BCF and VCF format. Additionally a log file is provided.
0
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
258
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
259 .. class:: infomark
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
260
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
261 **References**
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
262
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
263 @REFERENCES@
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
264 ]]></help>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
265 <expand macro="citations"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
266 </tool>