Mercurial > repos > iuc > delly_classify

comparison macros.xml @ 0:d3bc6ec7881f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
author iuc
date Fri, 22 Jan 2021 14:33:05 +0000
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children d31211a43b19
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-1:000000000000 0:d3bc6ec7881f
1 <?xml version="1.0"?>
2 <macros>
3 <token name="@TOOL_VERSION@">0.8.7</token>
4 <token name="@VERSION_SUFFIX@">0</token>
5 <xml name="requirements">
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">delly</requirement>
8 <requirement type="package" version="1.10.2">bcftools</requirement>
9 </requirements>
10 </xml>
11 <xml name="version_command">
12 <version_command><![CDATA[delly -v 2>&1 | grep 'Delly version' | cut -f 3 -d ' ']]></version_command>
13 </xml>
14 <xml name="citations">
15 <citations>
16 <citation type="doi">10.1093/bioinformatics/bts378</citation>
17 </citations>
18 </xml>
19
20 <!-- command -->
21
22 <token name="@BAM@"><![CDATA[
23 #for $i, $current in enumerate($input)
24 ln -s '${current}' 'input_${i}.bam' &&
25 ln -s '${current.metadata.bam_index}' 'input_${i}.bam.bai' &&
26 #end for
27 ]]></token>
28 <token name="@DUMP@"><![CDATA[
29 #if 'dump' in $oo.out
30 && test -f 'dump.tsv.gz' && bgzip -d 'dump.tsv.gz' || echo 'No dump file.'
31 #end if
32 ]]></token>
33 <token name="@LOG@"><![CDATA[
34 #if 'log' in $oo.out
35 |& tee '$out_log'
36 #end if
37 ]]></token>
38 <token name="@VCF@"><![CDATA[
39 #if 'vcf' in $oo.out
40 && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.'
41 #end if
42 ]]></token>
43
44 <!-- input -->
45
46 <xml name="cnoffset" token_default="">
47 <param name="cnoffset" type="float" min="0.0" max="1.0" value="@DEFAULT@" label="Set minimum CN offset" help="(--cn-offset)"/>
48 </xml>
49 <xml name="coverage" token_label="">
50 <param argument="--coverage" type="integer" value="10" label="@LABEL@"/>
51 </xml>
52 <xml name="exclude">
53 <param argument="--exclude" type="data" format="tabular" optional="true" label="Select file with regions to exclude"/>
54 </xml>
55 <xml name="genome">
56 <param argument="--genome" type="data" format="fasta" label="Select genome file"/>
57 </xml>
58 <xml name="genoqual">
59 <param name="genoqual" type="integer" value="5" label="Set minimum mapping quality for genotyping" help="(--geno-qual)"/>
60 </xml>
61 <xml name="input" token_format="" token_multiple="false" token_label="">
62 <param name="input" type="data" format="@FORMAT@" multiple="@MULTIPLE@" label="@LABEL@"/>
63 </xml>
64 <xml name="maxreadsep" token_default="">
65 <param argument="--maxreadsep" type="integer" value="@DEFAULT@" label="Set maximum read separation"/>
66 </xml>
67 <xml name="maxsize" token_default="" token_label="">
68 <param argument="--maxsize" type="integer" value="@DEFAULT@" label="@LABEL@"/>
69 </xml>
70 <xml name="minclip">
71 <param argument="--minclip" type="integer" value="25" label="Set minimum clipping length"/>
72 </xml>
73 <xml name="mincliquesize">
74 <param name="mincliquesize" type="integer" value="2" label="Set minimum paired-end/single-read clique size" help="(--min-clique-size)"/>
75 </xml>
76 <xml name="minrefsep" token_default="">
77 <param argument="--minrefsep" type="integer" value="@DEFAULT@" label="Set minimum reference separation"/>
78 </xml>
79 <xml name="minsize" token_default="" token_label="">
80 <param argument="--minsize" type="integer" value="@DEFAULT@" label="@LABEL@"/>
81 </xml>
82 <xml name="pass">
83 <param argument="--pass" type="boolean" truevalue="--pass" falsevalue="" label="Filter sites for PASS?"/>
84 </xml>
85 <xml name="ploidy">
86 <param argument="--ploidy" type="integer" value="2" label="Set baseline ploidy"/>
87 </xml>
88 <xml name="samples">
89 <param argument="--samples" type="data" format="tabular" label="Select sample file" help="Two-column sample file listing sample name and tumor or control."/>
90 </xml>
91 <xml name="svtype">
92 <param argument="--svtype" type="select" label="Select type(s) of structural variants to detect">
93 <option value="ALL" selected="true">All types (ALL)</option>
94 <option value="DEL">Deletion (DEL)</option>
95 <option value="DUP">Duplication (DUP)</option>
96 <option value="INS">Insertion (INS)</option>
97 <option value="INV">Inversion (INV)</option>
98 <option value="BND">Translocation (BND)</option>
99 </param>
100 </xml>
101 <xml name="vcffile">
102 <param argument="--vcffile" type="data" format="bcf,vcf" optional="true" label="Select genotyping file"/>
103 </xml>
104
105 <!-- output -->
106
107 <xml name="bcf">
108 <data name="out_bcf" format="bcf" from_work_dir="result.bcf" label="${tool.name} on ${on_string}: Result (BCF)">
109 <filter>'bcf' in oo['out']</filter>
110 </data>
111 </xml>
112 <xml name="vcf">
113 <data name="out_vcf" format="vcf" from_work_dir="result.vcf" label="${tool.name} on ${on_string}: Result (VCF)">
114 <filter>'vcf' in oo['out']</filter>
115 </data>
116 </xml>
117 <xml name="dump">
118 <data name="out_dump" format="tabular" from_work_dir="dump.tsv" label="${tool.name} on ${on_string}: SV-reads">
119 <filter>'dump' in oo['out']</filter>
120 </data>
121 </xml>
122 <xml name="log">
123 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
124 <filter>'log' in oo['out']</filter>
125 </data>
126 </xml>
127
128 <!-- help -->
129
130 <token name="@WID@"><![CDATA[
131 Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome.
132
133 Short-read SV calling
134
135 - *call* to discover and genotype structural variants
136 - *merge* structural variants across VCF/BCF files and within a single VCF/BCF file
137 - *filter* somatic or germline structural variants
138
139 Long-read SV calling
140
141 - *lr* for long-read SV discovery
142
143 Copy-number variant calling
144
145 - *cnv* to discover and genotype copy-number variants
146 - *classify* somatic or germline copy-number variants
147 ]]></token>
148 <token name="@REFERENCES@"><![CDATA[
149 More information are available on `GitHub <https://github.com/dellytools/delly>`_.
150 ]]></token>
151 </macros>