Mercurial > repos > iuc > delly_classify

comparison macros.xml.orig @ 1:148b595025b3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 08:00:10 +0000
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0:10b025ea9d24 1:148b595025b3
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 <<<<<<< HEAD
20
21 <!-- command -->
22 =======
23 <xml name="bio_tools">
24 <xrefs>
25 <xref type='bio.tools'>delly2</xref>
26 </xrefs>
27 </xml>
28 <!--
29 command
30 -->
31 >>>>>>> 20ed9dd6f (add bio.tools ID)
32
33 <token name="@BAM@"><![CDATA[
34 #for $i, $current in enumerate($input)
35 ln -s '${current}' 'input_${i}.bam' &&
36 ln -s '${current.metadata.bam_index}' 'input_${i}.bam.bai' &&
37 #end for
38 ]]></token>
39 <token name="@DUMP@"><![CDATA[
40 #if 'dump' in $oo.out
41 && test -f 'dump.tsv.gz' && bgzip -d 'dump.tsv.gz' || echo 'No dump file.'
42 #end if
43 ]]></token>
44 <token name="@LOG@"><![CDATA[
45 #if 'log' in $oo.out
46 |& tee '$out_log'
47 #end if
48 ]]></token>
49 <token name="@VCF@"><![CDATA[
50 #if 'vcf' in $oo.out
51 && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.'
52 #end if
53 ]]></token>
54
55 <!-- input -->
56
57 <xml name="cnoffset" token_default="">
58 <param name="cnoffset" type="float" min="0.0" max="1.0" value="@DEFAULT@" label="Set minimum CN offset" help="(--cn-offset)"/>
59 </xml>
60 <xml name="coverage" token_label="">
61 <param argument="--coverage" type="integer" value="10" label="@LABEL@"/>
62 </xml>
63 <xml name="exclude">
64 <param argument="--exclude" type="data" format="tabular" optional="true" label="Select file with regions to exclude"/>
65 </xml>
66 <xml name="genome">
67 <param argument="--genome" type="data" format="fasta" label="Select genome file"/>
68 </xml>
69 <xml name="genoqual">
70 <param name="genoqual" type="integer" value="5" label="Set minimum mapping quality for genotyping" help="(--geno-qual)"/>
71 </xml>
72 <xml name="input" token_format="" token_multiple="false" token_label="">
73 <param name="input" type="data" format="@FORMAT@" multiple="@MULTIPLE@" label="@LABEL@"/>
74 </xml>
75 <xml name="maxreadsep" token_default="">
76 <param argument="--maxreadsep" type="integer" value="@DEFAULT@" label="Set maximum read separation"/>
77 </xml>
78 <xml name="maxsize" token_default="" token_label="">
79 <param argument="--maxsize" type="integer" value="@DEFAULT@" label="@LABEL@"/>
80 </xml>
81 <xml name="minclip">
82 <param argument="--minclip" type="integer" value="25" label="Set minimum clipping length"/>
83 </xml>
84 <xml name="mincliquesize">
85 <param name="mincliquesize" type="integer" value="2" label="Set minimum paired-end/single-read clique size" help="(--min-clique-size)"/>
86 </xml>
87 <xml name="minrefsep" token_default="">
88 <param argument="--minrefsep" type="integer" value="@DEFAULT@" label="Set minimum reference separation"/>
89 </xml>
90 <xml name="minsize" token_default="" token_label="">
91 <param argument="--minsize" type="integer" value="@DEFAULT@" label="@LABEL@"/>
92 </xml>
93 <xml name="pass">
94 <param argument="--pass" type="boolean" truevalue="--pass" falsevalue="" label="Filter sites for PASS?"/>
95 </xml>
96 <xml name="ploidy">
97 <param argument="--ploidy" type="integer" value="2" label="Set baseline ploidy"/>
98 </xml>
99 <xml name="samples">
100 <param argument="--samples" type="data" format="tabular" label="Select sample file" help="Two-column sample file listing sample name and tumor or control."/>
101 </xml>
102 <xml name="svtype">
103 <param argument="--svtype" type="select" label="Select type(s) of structural variants to detect">
104 <option value="ALL" selected="true">All types (ALL)</option>
105 <option value="DEL">Deletion (DEL)</option>
106 <option value="DUP">Duplication (DUP)</option>
107 <option value="INS">Insertion (INS)</option>
108 <option value="INV">Inversion (INV)</option>
109 <option value="BND">Translocation (BND)</option>
110 </param>
111 </xml>
112 <xml name="vcffile">
113 <param argument="--vcffile" type="data" format="bcf,vcf" optional="true" label="Select genotyping file"/>
114 </xml>
115
116 <!-- output -->
117
118 <xml name="bcf">
119 <data name="out_bcf" format="bcf" from_work_dir="result.bcf" label="${tool.name} on ${on_string}: Result (BCF)">
120 <filter>'bcf' in oo['out']</filter>
121 </data>
122 </xml>
123 <xml name="vcf">
124 <data name="out_vcf" format="vcf" from_work_dir="result.vcf" label="${tool.name} on ${on_string}: Result (VCF)">
125 <filter>'vcf' in oo['out']</filter>
126 </data>
127 </xml>
128 <xml name="dump">
129 <data name="out_dump" format="tabular" from_work_dir="dump.tsv" label="${tool.name} on ${on_string}: SV-reads">
130 <filter>'dump' in oo['out']</filter>
131 </data>
132 </xml>
133 <xml name="log">
134 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
135 <filter>'log' in oo['out']</filter>
136 </data>
137 </xml>
138
139 <!-- help -->
140
141 <token name="@WID@"><![CDATA[
142 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.
143
144 Short-read SV calling
145
146 - *call* to discover and genotype structural variants
147 - *merge* structural variants across VCF/BCF files and within a single VCF/BCF file
148 - *filter* somatic or germline structural variants
149
150 Long-read SV calling
151
152 - *lr* for long-read SV discovery
153
154 Copy-number variant calling
155
156 - *cnv* to discover and genotype copy-number variants
157 - *classify* somatic or germline copy-number variants
158 ]]></token>
159 <token name="@REFERENCES@"><![CDATA[
160 More information are available on `GitHub <https://github.com/dellytools/delly>`_.
161 ]]></token>
162 </macros>