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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit beb2da7c9ef39a0b0ed0d508d7521468500a86a0
author iuc
date Fri, 19 Aug 2022 07:47:31 +0000
parents 7bd397ff21a2
children
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1 <?xml version="1.0"?>
1
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2 <tool id="delly_lr" name="Delly long-read (lr)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
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3 <description>optimized calling and genotyping of 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
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12 @BAM@
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13 @FASTA@
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14 ## run
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15 delly lr
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16 ## generic options
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17 --svtype $generic.svtype
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18 --technology $generic.technology
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19 --genome genome.fa
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20 #if $generic.exclude
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21 --exclude '$generic.exclude'
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22 #end if
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23 --outfile 'result.bcf'
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24 ## discovery options
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25 --mapqual $discovery.mapqual
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26 --minclip $discovery.minclip
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27 --min-clique-size $discovery.mincliquesize
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28 --minrefsep $discovery.minrefsep
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29 --maxreadsep $discovery.maxreadsep
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30 ## consensus options
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31 --max-reads $consensus.maxreads
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32 --flank-size $consensus.flanksize
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33 --flank-quality $consensus.flankquality
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34 ## genotyping options
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35 --geno-qual $genotyping.genoqual
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36 #if 'dump' in $oo.out
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37 --dump 'dump.tsv.gz'
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38 #end if
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39 ## input
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40 #for $i, $current in enumerate($input)
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41 'input_${i}.bam'
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42 #end for
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43
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44 ## postprocessing
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45 @LOG@
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46 @DUMP@
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47 @VCF@
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48 ]]></command>
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49 <inputs>
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50 <expand macro="input" format="bam" multiple="true" label="Select input file(s)"/>
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51 <section name="generic" title="Generic options" expanded="true">
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52 <expand macro="svtype"/>
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53 <param argument="--technology" type="select" label="Select sequencing technology">
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54 <option value="ont" selected="true">Oxford Nanopore (ont)</option>
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55 <option value="pb">PacBio (pb)</option>
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56 </param>
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57 <expand macro="genome"/>
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58 <expand macro="exclude"/>
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59 </section>
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60 <section name="discovery" title="Discovery options" expanded="true">
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61 <param argument="--mapqual" type="integer" value="10" label="Set minimum mapping quality"/>
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62 <expand macro="minclip"/>
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63 <expand macro="mincliquesize"/>
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64 <expand macro="minrefsep" default="30"/>
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65 <expand macro="maxreadsep" default="75"/>
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66 </section>
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67 <section name="consensus" title="Consensus options" expanded="true">
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68 <param name="maxreads" type="integer" value="5" label="Set maximum reads for consensus computation" help="(--max-reads)"/>
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69 <param name="flanksize" type="integer" value="400" label="Set minimum flank size" help="(--flank-size)"/>
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70 <param name="flankquality" type="float" min="0.0" max="1.0" value="0.9" label="Set minimum flank quality" help="(--flank-quality)"/>
0
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71 </section>
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72 <section name="genotyping" title="Genotyping options" expanded="true">
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73 <expand macro="genoqual"/>
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74 </section>
2
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75 <section name="oo" title="Output options" expanded="true">
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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="dump">SV-reads</option>
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80 <option value="vcf">VCF</option>
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81 </param>
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82 </section>
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83 </inputs>
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84 <outputs>
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85 <expand macro="bcf"/>
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86 <expand macro="dump"/>
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87 <expand macro="log"/>
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88 <expand macro="vcf"/>
0
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
89 </outputs>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
90 <tests>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
91 <!-- #1 default, single -->
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
92 <test expect_num_outputs="2">
2
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
93 <param name="input" value="normal.bam"/>
0
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
94 <section name="generic">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
95 <param name="genome" value="genome.fasta"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
96 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
97 <section name="oo">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
98 <param name="out" value="vcf,bcf"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
99 </section>
2
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
100 <output name="out_bcf">
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
101 <assert_contents>
4
7bd397ff21a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 57b50253f326baf18bfbf417d8c788b4f5ba66e6
iuc
parents: 3
diff changeset
102 <has_size value="1127" delta="10"/>
2
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
103 </assert_contents>
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
104 </output>
0
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
105 <output name="out_vcf">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
106 <assert_contents>
4
7bd397ff21a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 57b50253f326baf18bfbf417d8c788b4f5ba66e6
iuc
parents: 3
diff changeset
107 <has_n_lines n="46"/>
0
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
108 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;normal"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
109 </assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
110 </output>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
111 </test>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
112 <!-- #2 default, multi; test data to small, results are empty -->
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
113 <test expect_num_outputs="3">
2
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
114 <param name="input" value="normal.bam,tumor.bam"/>
0
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
115 <section name="generic">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
116 <param name="genome" value="genome.fasta"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
117 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
118 <section name="oo">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
119 <param name="out" value="vcf,bcf,log"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
120 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
121 <output name="out_bcf">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
122 <assert_contents>
4
7bd397ff21a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 57b50253f326baf18bfbf417d8c788b4f5ba66e6
iuc
parents: 3
diff changeset
123 <has_size value="1131" delta="10"/>
0
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
124 </assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
125 </output>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
126 <output name="out_log">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
127 <assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
128 <has_text_matching expression=".+Done.+"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
129 </assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
130 </output>
2
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
131 <output name="out_vcf">
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
132 <assert_contents>
5
97f649646cc1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit beb2da7c9ef39a0b0ed0d508d7521468500a86a0
iuc
parents: 4
diff changeset
133 <has_n_lines n="46"/>
2
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
134 </assert_contents>
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
135 </output>
0
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
136 </test>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
137 <!-- #3 -->
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
138 <test expect_num_outputs="4">
2
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
139 <param name="input" value="normal.bam"/>
0
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
140 <section name="generic">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
141 <param name="genome" value="genome.fasta"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
142 <param name="exclude" value="exclude.tsv"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
143 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
144 <section name="oo">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
145 <param name="out" value="vcf,bcf,dump,log"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
146 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
147 <output name="out_bcf">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
148 <assert_contents>
4
7bd397ff21a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 57b50253f326baf18bfbf417d8c788b4f5ba66e6
iuc
parents: 3
diff changeset
149 <has_size value="1127" delta="10"/>
0
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
150 </assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
151 </output>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
152 <output name="out_dump">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
153 <assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
154 <has_n_lines n="0"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
155 </assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
156 </output>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
157 <output name="out_log">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
158 <assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
159 <has_text_matching expression=".+Done.+"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
160 </assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
161 </output>
2
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
162 <output name="out_vcf">
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
163 <assert_contents>
4
7bd397ff21a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 57b50253f326baf18bfbf417d8c788b4f5ba66e6
iuc
parents: 3
diff changeset
164 <has_n_lines n="46"/>
2
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
165 </assert_contents>
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
166 </output>
0
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
167 </test>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
168 <!-- #4 -->
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
169 <test expect_num_outputs="4">
2
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
170 <param name="input" value="normal.bam"/>
0
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
171 <section name="generic">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
172 <param name="genome" value="genome.fasta"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
173 <param name="svtype" value="DEL"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
174 <param name="technology" value="pb"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
175 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
176 <section name="discovery">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
177 <param name="mapqual" value="2"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
178 <param name="qualtra" value="19"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
179 <param name="madcutoff" value="8"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
180 <param name="minclip" value="24"/>
1
d5124d5c8131 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
181 <param name="mincliquesize" value="1"/>
0
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
182 <param name="minrefsep" value="24"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
183 <param name="maxreadsep" value="39"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
184 </section>
2
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
185 <section name="consensus">
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
186 <param name="maxreads" value="6"/>
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
187 <param name="flanksize" value="399"/>
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
188 <param name="flankquality" value="0.91"/>
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
189 </section>
0
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
190 <section name="genotyping">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
191 <param name="genoqual" value="4"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
192 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
193 <section name="oo">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
194 <param name="out" value="vcf,bcf,dump,log"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
195 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
196 <output name="out_bcf">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
197 <assert_contents>
4
7bd397ff21a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 57b50253f326baf18bfbf417d8c788b4f5ba66e6
iuc
parents: 3
diff changeset
198 <has_size value="1127" delta="10"/>
0
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
199 </assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
200 </output>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
201 <output name="out_dump">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
202 <assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
203 <has_size value="0"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
204 </assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
205 </output>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
206 <output name="out_log">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
207 <assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
208 <has_text_matching expression=".+"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
209 </assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
210 </output>
2
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
211 <output name="out_vcf">
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
212 <assert_contents>
4
7bd397ff21a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 57b50253f326baf18bfbf417d8c788b4f5ba66e6
iuc
parents: 3
diff changeset
213 <has_n_lines n="46"/>
2
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
214 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;normal"/>
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
215 </assert_contents>
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
216 </output>
0
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
217 </test>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
218 <!-- #5 -->
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
219 <test expect_num_outputs="1">
2
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
220 <param name="input" value="normal.bam"/>
0
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
221 <section name="generic">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
222 <param name="genome" value="genome.fasta"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
223 <param name="svtype" value="INS"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
224 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
225 <section name="oo">
629a0066003d "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"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
227 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
228 <output name="out_vcf">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
229 <assert_contents>
4
7bd397ff21a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 57b50253f326baf18bfbf417d8c788b4f5ba66e6
iuc
parents: 3
diff changeset
230 <has_n_lines n="46"/>
0
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
231 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;normal"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
232 </assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
233 </output>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
234 </test>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
235 <!-- #6 -->
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
236 <test expect_num_outputs="1">
2
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
237 <param name="input" value="normal.bam"/>
0
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
238 <section name="generic">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
239 <param name="genome" value="genome.fasta"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
240 <param name="svtype" value="DUP"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
241 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
242 <section name="oo">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
243 <param name="out" value="bcf"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
244 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
245 <output name="out_bcf">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
246 <assert_contents>
4
7bd397ff21a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 57b50253f326baf18bfbf417d8c788b4f5ba66e6
iuc
parents: 3
diff changeset
247 <has_size value="1127" delta="10"/>
0
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
248 </assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
249 </output>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
250 </test>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
251 <!-- #7 -->
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
252 <test expect_num_outputs="1">
2
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
253 <param name="input" value="normal.bam"/>
0
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
254 <section name="generic">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
255 <param name="genome" value="genome.fasta"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
256 <param name="svtype" value="INV"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
257 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
258 <section name="oo">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
259 <param name="out" value="dump"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
260 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
261 <output name="out_dump">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
262 <assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
263 <has_size value="0"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
264 </assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
265 </output>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
266 </test>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
267 <!-- #8 -->
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
268 <test expect_num_outputs="1">
2
ceda4714f3a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
iuc
parents: 1
diff changeset
269 <param name="input" value="normal.bam"/>
0
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
270 <section name="generic">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
271 <param name="genome" value="genome.fasta"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
272 <param name="svtype" value="BND"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
273 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
274 <section name="oo">
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275 <param name="out" value="log"/>
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276 </section>
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277 <output name="out_log">
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278 <assert_contents>
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279 <has_text_matching expression=".+"/>
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280 </assert_contents>
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281 </output>
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282 </test>
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283 </tests>
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284 <help><![CDATA[
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285 .. class:: infomark
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286
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287 **What it does**
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288
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289 @WID@
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290
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291 **Input**
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292
2
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293 Delly *long-read (lr)* needs a sorted, indexed and duplicate marked BAM file for every input sample. An indexed reference genome is required to identify split-reads.
0
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294
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295 **Output**
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296
2
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297 The output is available in BCF and VCF format. Additionally an output file for SV-reads and a log file are provided.
0
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298
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299 .. class:: infomark
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300
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301 **References**
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302
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303 @REFERENCES@
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304 ]]></help>
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305 <expand macro="citations"/>
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306 </tool>