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comparison macros.xml @ 0:8fff33666441 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
author iuc
date Thu, 29 Oct 2020 20:48:48 +0000
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-1:000000000000 0:8fff33666441
1 <?xml version="1.0"?>
2 <macros>
3 <token name="@TOOL_VERSION@">0.8.5</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 <!--
21 command
22 -->
23
24 <token name="@BAM@"><![CDATA[
25 #for $i, $current in enumerate($samples)
26 ln -s '${current}' 'sample_${i}.bam' &&
27 ln -s '${current.metadata.bam_index}' 'sample_${i}.bam.bai' &&
28 #end for
29 ]]></token>
30 <token name="@DUMP@"><![CDATA[
31 #if 'dump' in $oo.out
32 && test -f 'dump.tsv.gz' && bgzip -d 'dump.tsv.gz' || echo 'No dump file.'
33 #end if
34 ]]></token>
35 <token name="@LOG@"><![CDATA[
36 #if 'log' in $oo.out
37 |& tee '$out_log'
38 #end if
39 ]]></token>
40 <token name="@VCF@"><![CDATA[
41 #if 'vcf' in $oo.out
42 && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.'
43 #end if
44 ]]></token>
45
46 <!--
47 input
48 -->
49
50 <xml name="exclude">
51 <param argument="--exclude" type="data" format="tabular" optional="true" label="Select file with regions to exclude"/>
52 </xml>
53 <xml name="genome">
54 <param argument="--genome" type="data" format="fasta" label="Select genome"/>
55 </xml>
56 <xml name="genoqual">
57 <param name="genoqual" type="integer" value="5" label="Set minimum mapping quality for genotyping" help="(--geno-qual)"/>
58 </xml>
59 <xml name="minclip">
60 <param argument="--minclip" type="integer" value="25" label="Set minimum clipping length"/>
61 </xml>
62 <xml name="maxreadsep" token_default="40">
63 <param argument="--maxreadsep" type="integer" value="@DEFAULT@" label="Set maximum read separation"/>
64 </xml>
65 <xml name="maxsize" token_default="1000000">
66 <param argument="--maxsize" type="integer" value="@DEFAULT@" label="Set maximum SV size"/>
67 </xml>
68 <xml name="mincliquesize">
69 <param name="mincliquesize" type="integer" value="2" label="Set minimum min. PE/SR clique size" help="(--min-clique-size)"/>
70 </xml>
71 <xml name="minrefsep" token_default="25">
72 <param argument="--minrefsep" type="integer" value="@DEFAULT@" label="Set minimum reference separation"/>
73 </xml>
74 <xml name="minsize">
75 <param argument="--minsize" type="integer" value="0" label="Set minimum SV size"/>
76 </xml>
77 <xml name="samples" token_format="bam" token_multiple="true" token_label="Select sample file(s)">
78 <param name="samples" type="data" format="@FORMAT@" multiple="@MULTIPLE@" label="@LABEL@"/>
79 </xml>
80 <xml name="svtype">
81 <param argument="--svtype" type="select" label="Select type(s) of structural variants to detect">
82 <option value="ALL" selected="true">All types (ALL)</option>
83 <option value="DEL">Deletion (DEL)</option>
84 <option value="INS">Insertion (INS)</option>
85 <option value="DUP">Duplication (DUP)</option>
86 <option value="INV">Inversion (INV)</option>
87 <option value="BND">Translocation (BND)</option>
88 </param>
89 </xml>
90 <xml name="vcffile">
91 <param argument="--vcffile" type="data" format="vcf,bcf" optional="true" label="Select genotyping file"/>
92 </xml>
93
94 <!--
95 output
96 -->
97
98 <xml name="vcf">
99 <data name="out_vcf" format="vcf" from_work_dir="result.vcf" label="${tool.name} on ${on_string}: Result (VCF)">
100 <filter>'vcf' in oo['out']</filter>
101 </data>
102 </xml>
103 <xml name="bcf">
104 <data name="out_bcf" format="bcf" from_work_dir="result.bcf" label="${tool.name} on ${on_string}: Result (BCF)">
105 <filter>'bcf' in oo['out']</filter>
106 </data>
107 </xml>
108 <xml name="dump">
109 <data name="out_dump" format="tabular" from_work_dir="dump.tsv" label="${tool.name} on ${on_string}: SV-reads">
110 <filter>'dump' in oo['out']</filter>
111 </data>
112 </xml>
113 <xml name="log">
114 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
115 <filter>'log' in oo['out']</filter>
116 </data>
117 </xml>
118
119 <!--
120 Help
121 -->
122
123 <token name="@WID@"><![CDATA[
124 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.
125 ]]></token>
126 <token name="@REFERENCES@"><![CDATA[
127 More information are available on `GitHub <https://github.com/dellytools/delly>`_.
128 ]]></token>
129 </macros>