Mercurial > repos > iuc > delly_filter

annotate filter.xml @ 1:9919057a466c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
author iuc
date Thu, 29 Oct 2020 20:50:57 +0000
parents a75e05f20a66
children 6184cfc70e28
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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">
0
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3 <description>somatic or germline structural variants</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="version_command"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 ## initialize
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11 #if $samples.is_of_type('vcf')
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12 bcftools view -Ob '$samples' > 'sample.bcf.gz' &&
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13 bcftools index 'sample.bcf.gz' &&
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14 #else
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15 ln -s '${samples}' 'sample.bcf.gz' &&
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16 ln -s '${samples.metadata.bcf_index}' 'sample.bcf.gz.csi' &&
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17 #end if
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18
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19 ## run
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20 delly filter
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21 ## generic options
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22 --filter $sv.mode_cond.mode_sel
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23 --outfile 'result.bcf'
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24 --altaf $generic.altaf
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25 --minsize $generic.minsize
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26 --maxsize $generic.maxsize
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27 --ratiogeno $generic.ratiogeno
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28 $generic.pass
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29 ## somatic options
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30 #if $sv.mode_cond.mode_sel == 'somatic'
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31 --samples '$sv.mode_cond.samples'
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32 --coverage $sv.mode_cond.coverage
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33 --controlcontamination $sv.mode_cond.controlcontamination
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34 #end if
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35 ## germline options
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36 #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 ## samples
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42 'sample.bcf.gz' ## input
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43
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44 ## postprocessing
1
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45 @LOG@
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46 @VCF@
0
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47 ]]></command>
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48 <inputs>
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49 <expand macro="samples" format="bcf,vcf" multiple="false" label="Select 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"/>
1
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52 <expand macro="minsize"/>
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53 <expand macro="maxsize" default="500000000"/>
0
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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">
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59 <param argument="mode_sel" type="select" label="Select filter mode">
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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">
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64 <param argument="--samples" type="data" format="tabular" label="Select sample file" help="Two-column sample file listing sample name and tumor or control."/>
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65 <param argument="--coverage" type="integer" value="10" 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>
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75 <section name="oo" title="Output options">
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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>
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78 <option value="vcf">VCF</option>
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79 <option value="log">Log</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="vcf"/>
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85 <expand macro="bcf"/>
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86 <expand macro="log"/>
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87 </outputs>
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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">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
91 <param name="samples" value="call_1.bcf.gz"/>
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">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
116 <param name="samples" value="call_1.bcf.gz"/>
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>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
140 <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
141 <assert_contents>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
142 <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
143 <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
144 <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
145 </assert_contents>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
146 </output>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
147 <output name="out_log">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
148 <assert_contents>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
149 <has_text_matching expression=".+Done\."/>
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">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
155 <param name="samples" value="call_1.bcf.gz"/>
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">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
179 <param name="samples" value="call_1.bcf.gz"/>
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>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
203 <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
204 <assert_contents>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
205 <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
206 <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
207 <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
208 </assert_contents>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
209 </output>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
210 <output name="out_log">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
211 <assert_contents>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
212 <has_text_matching expression=".+Done\."/>
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">
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
218 <param name="samples" value="call_1.vcf.gz"/>
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>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
230 <has_size value="2440" delta="10"/>
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>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
235 <has_n_lines n="142"/>
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
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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 Delly *filter* contains workflows for germline and somatic SV calling.
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 **Input**
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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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 *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
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diff changeset
254
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
255 *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
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diff changeset
256
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
257 **Output**
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 The output is available in BCF and VCF format.
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 .. class:: infomark
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
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diff changeset
264
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
265 @REFERENCES@
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
266 ]]></help>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
267 <expand macro="citations"/>
a75e05f20a66 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
268 </tool>