Mercurial > repos > iuc > delly_merge

annotate merge.xml @ 1:97c7441aed0d 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 20:51:37 +0000
parents 6331d804f983
children 148389992630
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6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
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1 <?xml version="1.0"?>
1
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2 <tool id="delly_merge" name="Delly merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
0
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3 <description>structural variants across/within VCF/BCF file(s)</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 #for $i, $current in enumerate($samples)
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12 #if $current.is_of_type('vcf')
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13 bcftools view -Ob '$current' > 'sample_${i}.bcf.gz' &&
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14 bcftools index 'sample_${i}.bcf.gz' &&
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15 #else
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16 ln -s '${current}' 'sample_${i}.bcf.gz' &&
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17 ln -s '${current.metadata.bcf_index}' 'sample_${i}.bcf.gz.csi' &&
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18 #end if
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19 #end for
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20
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21 ## run
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22 delly merge
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23 ## generic options
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24 --outfile 'result.bcf'
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25 --chunks $generic.chunks
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26 --vaf $generic.vaf
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27 --coverage $generic.coverage
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28 --minsize $generic.minsize
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29 --maxsize $generic.maxsize
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30 $generic.precise
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31 $generic.pass
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32 ## overlap options
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33 --bp-offset $overlap.bpoffset
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34 --rec-overlap $overlap.recoverlap
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35 ## samples
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36 #for $i, $current in enumerate($samples)
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37 'sample_${i}.bcf.gz'
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38 #end for
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39
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40 ## postprocessing
1
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41 @LOG@
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42 @VCF@
0
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43 ]]></command>
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44 <inputs>
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45 <expand macro="samples" format="bcf,vcf"/>
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46 <section name="generic" title="Generic options" expanded="true">
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47 <param argument="--chunks" type="integer" value="500" label="Set maximum chunk size to merge groups of BCF files"/>
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48 <param argument="--vaf" type="float" value="0.15" min="0.0" max="1.0" label="Set minimum fractional ALT support"/>
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49 <param argument="--coverage" type="integer" value="10" label="Set minimum coverage"/>
1
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50 <expand macro="minsize"/>
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51 <expand macro="maxsize"/>
0
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52 <param argument="--precise" type="boolean" truevalue="--precise" falsevalue="" label="Filter sites for PRECISE?"/>
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53 <param argument="--pass" type="boolean" truevalue="--pass" falsevalue="" label="Filter sites for PASS?"/>
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54 </section>
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55 <section name="overlap" title="Overlap options" expanded="true">
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56 <param name="bpoffset" type="integer" value="1000" label="Set maximum breakpoint offset" help="(--bp-offset)"/>
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57 <param name="recoverlap" type="float" value="0.8" label="Set minimum reciprocal overlap" help="(--rec-overlap)"/>
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58 </section>
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59 <section name="oo" title="Output options">
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60 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">
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61 <option value="bcf" selected="true">BCF</option>
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62 <option value="vcf">VCF</option>
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63 <option value="log">Log</option>
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64 </param>
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65 </section>
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66 </inputs>
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67 <outputs>
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68 <expand macro="vcf"/>
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69 <expand macro="bcf"/>
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70 <expand macro="log"/>
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71 </outputs>
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72 <tests>
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73 <!-- #1 default, bcf -->
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74 <test expect_num_outputs="2">
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75 <param name="samples" value="call_1.bcf.gz,call_2.bcf.gz"/>
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76 <section name="oo">
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77 <param name="out" value="vcf,bcf"/>
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78 </section>
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79 <output name="out_bcf">
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80 <assert_contents>
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81 <has_size value="1851" delta="10"/>
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82 </assert_contents>
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83 </output>
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84 <output name="out_vcf">
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85 <assert_contents>
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86 <has_n_lines n="128"/>
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87 <has_line line="##fileformat=VCFv4.2"/>
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88 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO"/>
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89 </assert_contents>
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diff changeset
90 </output>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
91 </test>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
92 <!-- #2 bcf-->
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
93 <test expect_num_outputs="3">
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
94 <param name="samples" value="call_1.bcf.gz,call_2.bcf.gz"/>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
95 <section name="generic">
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
96 <param name="chunks" value="500"/>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
97 <param name="vaf" value="0.16"/>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
98 <param name="coverage" value="10"/>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
99 <param name="minsize" value="0"/>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
100 <param name="maxsize" value="1000000"/>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
101 <param name="precise" value="true"/>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
102 <param name="pass" value="true"/>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
103 </section>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
104 <section name="overlap">
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
105 <param name="bp-offset" value="1000"/>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
106 <param name="rec-overlap" value="0.79"/>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
107 </section>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
108 <section name="oo">
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
109 <param name="out" value="vcf,bcf,log"/>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
110 </section>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
111 <output name="out_bcf">
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
112 <assert_contents>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
113 <has_size value="1851" delta="10"/>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
114 </assert_contents>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
115 </output>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
116 <output name="out_vcf">
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
117 <assert_contents>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
118 <has_n_lines n="128"/>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
119 <has_line line="##fileformat=VCFv4.2"/>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
120 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO"/>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
121 <has_text_matching expression="chr5&#009;75911568.+"/>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
122 </assert_contents>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
123 </output>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
124 <output name="out_log">
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
125 <assert_contents>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
126 <has_text_matching expression=".+Done\."/>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
127 </assert_contents>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
128 </output>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
129 </test>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
130 <!-- #3 default, vcf -->
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
131 <test expect_num_outputs="2">
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
132 <param name="samples" value="call_1.vcf.gz,call_2.vcf.gz"/>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
133 <section name="oo">
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
134 <param name="out" value="vcf,bcf"/>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
135 </section>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
136 <output name="out_bcf">
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
137 <assert_contents>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
138 <has_size value="1851" delta="10"/>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
139 </assert_contents>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
140 </output>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
141 <output name="out_vcf">
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
142 <assert_contents>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
143 <has_n_lines n="128"/>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
144 <has_line line="##fileformat=VCFv4.2"/>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
145 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO"/>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
146 </assert_contents>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
147 </output>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
148 </test>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
149 </tests>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
150 <help><![CDATA[
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
151 .. class:: infomark
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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152
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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153 **What it does**
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
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154
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
155 @WID@
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
156
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
157 Delly *merge* merges SV sites into a unified site list.
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
158
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
159 **Input**
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
160
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
161 BCF or VCF files.
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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162
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
163 **Output**
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
164
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
165 A single BCF file.
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
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166
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
167 .. class:: infomark
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
168
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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169 **References**
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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170
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
171 @REFERENCES@
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
172 ]]></help>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
173 <expand macro="citations"/>
6331d804f983 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
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diff changeset
174 </tool>