Mercurial > repos > iuc > delly_call

comparison macros.xml @ 0:e15927444573 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 07:43:20 +0000
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children c027f82af2fb
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-1:000000000000 0:e15927444573
1 <?xml version="1.0"?>
2 <macros>
3 <token name="@TOOL_VERSION@">0.8.3</token>
4 <token name="@DESCRIPTION@"></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 <!--
21 input
22 -->
23
24 <xml name="exclude">
25 <param argument="--exclude" type="data" format="tabular" optional="true" label="Select file with regions to exclude"/>
26 </xml>
27 <xml name="genome">
28 <param argument="--genome" type="data" format="fasta" label="Select genome"/>
29 </xml>
30 <xml name="genoqual">
31 <param name="genoqual" type="integer" value="5" label="Set minimum mapping quality for genotyping" help="(--geno-qual)"/>
32 </xml>
33 <xml name="minclip">
34 <param argument="--minclip" type="integer" value="25" label="Set minimum clipping length"/>
35 </xml>
36 <xml name="maxreadsep">
37 <param argument="--maxreadsep" type="integer" value="40" label="Set maximum read separation"/>
38 </xml>
39 <xml name="minrefsep">
40 <param argument="--minrefsep" type="integer" value="25" label="Set minimum reference separation"/>
41 </xml>
42 <xml name="samples" token_format="bam" token_multiple="true" token_label="Select sample file(s)">
43 <param name="samples" type="data" format="@FORMAT@" multiple="@MULTIPLE@" label="@LABEL@"/>
44 </xml>
45 <xml name="svtype">
46 <param argument="--svtype" type="select" label="Select type(s) of structural variants to detect">
47 <option value="ALL" selected="true">All types (ALL)</option>
48 <option value="DEL">Deletion (DEL)</option>
49 <option value="INS">Insertion (INS)</option>
50 <option value="DUP">Duplication (DUP)</option>
51 <option value="INV">Inversion (INV)</option>
52 <option value="BND">Translocation (BND)</option>
53 </param>
54 </xml>
55 <xml name="vcffile">
56 <param argument="--vcffile" type="data" format="vcf,bcf" optional="true" label="Select genotyping file"/>
57 </xml>
58
59 <!--
60 output
61 -->
62
63 <xml name="vcf">
64 <data name="out_vcf" format="vcf" from_work_dir="result.vcf" label="${tool.name} on ${on_string}: Result (VCF)">
65 <filter>'vcf' in oo['out']</filter>
66 </data>
67 </xml>
68 <xml name="bcf">
69 <data name="out_bcf" format="bcf" from_work_dir="result.bcf" label="${tool.name} on ${on_string}: Result (BCF)">
70 <filter>'bcf' in oo['out']</filter>
71 </data>
72 </xml>
73 <xml name="dump">
74 <data name="out_dump" format="tabular" from_work_dir="dump.tsv" label="${tool.name} on ${on_string}: SV-reads">
75 <filter>'dump' in oo['out']</filter>
76 </data>
77 </xml>
78 <xml name="log">
79 <data name="out_log" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: Log">
80 <filter>'log' in oo['out']</filter>
81 </data>
82 </xml>
83
84 <!--
85 Help
86 -->
87
88 <token name="@WID@"><![CDATA[
89 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.
90 ]]></token>
91 <token name="@REFERENCES@"><![CDATA[
92 More information are available on `github <https://github.com/dellytools/delly>`_.
93 ]]></token>
94 </macros>