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annotate lr.xml @ 0:629a0066003d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
author iuc
date Mon, 28 Sep 2020 07:45:41 +0000
parents
children d5124d5c8131
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0
629a0066003d "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"?>
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2 <tool id="delly_lr" name="Delly long-read (lr)" version="@TOOL_VERSION@+galaxy0" profile="18.01">
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3 <description>optimized calling and genotyping of 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 #for $i, $current in enumerate($samples)
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12 ln -s '${current}' 'sample_${i}.bam' &&
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13 ln -s '${current.metadata.bam_index}' 'sample_${i}.bam.bai' &&
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14 #end for
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15
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16 ## run
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17 delly lr
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18 ## generic options
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19 --svtype $generic.svtype
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20 --technology $generic.technology
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21 --genome '$generic.genome'
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22 #if $generic.exclude
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23 --exclude '$generic.exclude'
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24 #end if
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25 --outfile 'result.bcf'
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26 ## discovery options
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27 --mapqual $discovery.mapqual
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28 --minclip $discovery.minclip
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29 --minrefsep $discovery.minrefsep
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30 --maxreadsep $discovery.maxreadsep
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31 ## genotyping options
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32 #if $genotyping.vcffile
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33 --vcffile '$genotyping.vcffile'
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34 #end if
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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 ## samples
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40 #for $i, $current in enumerate($samples)
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41 'sample_${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 #if 'log' in $oo.out
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46 |& tee 'log.txt'
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47 #end if
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48 #if 'vcf' in $oo.out
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49 && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.'
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50 #end if
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51 #if 'dump' in $oo.out
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52 && test -f 'dump.tsv.gz' && bgzip -d 'dump.tsv.gz' || echo 'No dump file.'
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53 #end if
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54 ]]></command>
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55 <inputs>
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56 <expand macro="samples"/>
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57 <section name="generic" title="Generic options" expanded="true">
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58 <expand macro="genome"/>
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59 <expand macro="svtype"/>
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60 <expand macro="exclude"/>
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61 <param argument="--technology" type="select" label="Select sequencing technology">
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62 <option value="ont" selected="true">Oxford Nanopore (ont)</option>
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63 <option value="pb">Pacbio (pb)</option>
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64 </param>
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65 </section>
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66 <section name="discovery" title="Discovery options" expanded="true">
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67 <param argument="--mapqual" type="integer" value="1" label="Set minimum mapping quality"/>
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68 <expand macro="minclip"/>
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69 <expand macro="minrefsep"/>
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70 <expand macro="maxreadsep"/>
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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="vcffile"/>
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74 <expand macro="genoqual"/>
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75 </section>
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76 <section name="oo" title="Output options">
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77 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">
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78 <option value="bcf" selected="true">BCF</option>
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79 <option value="vcf">VCF</option>
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80 <option value="dump">SV-reads</option>
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81 <option value="log">Log</option>
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82 </param>
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83 </section>
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84 </inputs>
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85 <outputs>
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86 <expand macro="vcf"/>
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87 <expand macro="bcf"/>
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88 <expand macro="dump"/>
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89 <expand macro="log"/>
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90 </outputs>
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91 <tests>
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92 <!-- no test implemented for parameter vcffile -->
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
93
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
94 <!-- #1 default, single -->
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
95 <test expect_num_outputs="2">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
96 <param name="samples" value="normal.bam"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
97 <section name="generic">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
98 <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
99 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
100 <section name="oo">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
101 <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
102 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
103 <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
104 <assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
105 <has_size value="3661" delta="10"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
106 <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
107 </assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
108 </output>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
109 <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
110 <assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
111 <has_size value="1184" delta="10"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
112 </assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
113 </output>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
114 </test>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
115 <!-- #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
116 <test expect_num_outputs="3">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
117 <param name="samples" value="normal.bam,tumor.bam"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
118 <section name="generic">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
119 <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
120 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
121 <section name="oo">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
122 <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
123 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
124 <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
125 <assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
126 <has_size value="3667" delta="10"/>
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 </output>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
129 <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
130 <assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
131 <has_size value="1189" delta="10"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
132 </assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
133 </output>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
134 <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
135 <assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
136 <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
137 </assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
138 </output>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
139 </test>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
140 <!-- #3 -->
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
141 <test expect_num_outputs="4">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
142 <param name="samples" value="normal.bam"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
143 <section name="generic">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
144 <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
145 <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
146 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
147 <section name="oo">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
148 <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
149 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
150 <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
151 <assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
152 <has_size value="3661" delta="10"/>
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 </output>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
155 <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
156 <assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
157 <has_size value="1186" delta="10"/>
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 </output>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
160 <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
161 <assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
162 <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
163 </assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
164 </output>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
165 <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
166 <assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
167 <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
168 </assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
169 </output>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
170 </test>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
171 <!-- #4 -->
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
172 <test expect_num_outputs="4">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
173 <param name="samples" value="normal.bam"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
174 <section name="generic">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
175 <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
176 <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
177 <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
178 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
179 <section name="discovery">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
180 <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
181 <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
182 <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
183 <param name="minclip" value="24"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
184 <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
185 <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
186 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
187 <section name="genotyping">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
188 <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
189 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
190 <section name="oo">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
191 <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
192 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
193 <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
194 <assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
195 <has_size value="1182" delta="10"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
196 </assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
197 </output>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
198 <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
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 <has_size value="3661" delta="10"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
201 <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
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 </output>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
204 <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
205 <assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
206 <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
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 </output>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
209 <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
210 <assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
211 <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
212 </assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
213 </output>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
214 </test>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
215 <!-- #5 -->
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
216 <test expect_num_outputs="1">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
217 <param name="samples" value="normal.bam"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
218 <section name="generic">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
219 <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
220 <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
221 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
222 <section name="oo">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
223 <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
224 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
225 <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
226 <assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
227 <has_size value="3661" delta="10"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
228 <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
229 </assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
230 </output>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
231 </test>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
232 <!-- #6 -->
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
233 <test expect_num_outputs="1">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
234 <param name="samples" value="normal.bam"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
235 <section name="generic">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
236 <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
237 <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
238 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
239 <section name="oo">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
240 <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
241 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
242 <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
243 <assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
244 <has_size value="1182" delta="10"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
245 </assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
246 </output>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
247 </test>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
248 <!-- #7 -->
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
249 <test expect_num_outputs="1">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
250 <param name="samples" value="normal.bam"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
251 <section name="generic">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
252 <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
253 <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
254 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
255 <section name="oo">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
256 <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
257 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
258 <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
259 <assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
260 <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
261 </assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
262 </output>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
263 </test>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
264 <!-- #8 -->
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
265 <test expect_num_outputs="1">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
266 <param name="samples" value="normal.bam"/>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
267 <section name="generic">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
268 <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
269 <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
270 </section>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
271 <section name="oo">
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
272 <param name="out" value="log"/>
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 <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
275 <assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
276 <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
277 </assert_contents>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
278 </output>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
279 </test>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
280 </tests>
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
281 <help><![CDATA[
629a0066003d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
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282 .. class:: infomark
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283
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284 **What it does**
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285
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286 @WID@
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287
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288 Delly *lr* uses the long-read SV discovery mode.
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289
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290 **Input**
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291
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292 Delly *lr* needs a sorted, indexed and duplicate marked BAM file for every input sample. An indexed reference genome is required to identify split-reads. Additionally a VCF/BCF file for genotyping can be applied.
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293
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294 **Output**
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295
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296 The output is available in BCF and VCF format. Additionally a output file for SV-reads is provided.
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297
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298 .. class:: infomark
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299
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300 **References**
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301
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302 @REFERENCES@
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303 ]]></help>
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304 <expand macro="citations"/>
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305 </tool>