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comparison macros.xml @ 2:445e356988a7 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 14:28:59 +0000
parents c559b5bb484b
children db71f8a3323a
comparison
equal deleted inserted replaced
1:c559b5bb484b 2:445e356988a7
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@TOOL_VERSION@">0.8.5</token> 3 <token name="@TOOL_VERSION@">0.8.7</token>
4 <token name="@VERSION_SUFFIX@">0</token> 4 <token name="@VERSION_SUFFIX@">0</token>
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">delly</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">delly</requirement>
8 <requirement type="package" version="1.10.2">bcftools</requirement> 8 <requirement type="package" version="1.10.2">bcftools</requirement>
15 <citations> 15 <citations>
16 <citation type="doi">10.1093/bioinformatics/bts378</citation> 16 <citation type="doi">10.1093/bioinformatics/bts378</citation>
17 </citations> 17 </citations>
18 </xml> 18 </xml>
19 19
20 <!-- 20 <!-- command -->
21 command
22 -->
23 21
24 <token name="@BAM@"><![CDATA[ 22 <token name="@BAM@"><![CDATA[
25 #for $i, $current in enumerate($samples) 23 #for $i, $current in enumerate($input)
26 ln -s '${current}' 'sample_${i}.bam' && 24 ln -s '${current}' 'input_${i}.bam' &&
27 ln -s '${current.metadata.bam_index}' 'sample_${i}.bam.bai' && 25 ln -s '${current.metadata.bam_index}' 'input_${i}.bam.bai' &&
28 #end for 26 #end for
29 ]]></token> 27 ]]></token>
30 <token name="@DUMP@"><![CDATA[ 28 <token name="@DUMP@"><![CDATA[
31 #if 'dump' in $oo.out 29 #if 'dump' in $oo.out
32 && test -f 'dump.tsv.gz' && bgzip -d 'dump.tsv.gz' || echo 'No dump file.' 30 && test -f 'dump.tsv.gz' && bgzip -d 'dump.tsv.gz' || echo 'No dump file.'
41 #if 'vcf' in $oo.out 39 #if 'vcf' in $oo.out
42 && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.' 40 && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.'
43 #end if 41 #end if
44 ]]></token> 42 ]]></token>
45 43
46 <!-- 44 <!-- input -->
47 input
48 -->
49 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>
50 <xml name="exclude"> 52 <xml name="exclude">
51 <param argument="--exclude" type="data" format="tabular" optional="true" label="Select file with regions to exclude"/> 53 <param argument="--exclude" type="data" format="tabular" optional="true" label="Select file with regions to exclude"/>
52 </xml> 54 </xml>
53 <xml name="genome"> 55 <xml name="genome">
54 <param argument="--genome" type="data" format="fasta" label="Select genome"/> 56 <param argument="--genome" type="data" format="fasta" label="Select genome file"/>
55 </xml> 57 </xml>
56 <xml name="genoqual"> 58 <xml name="genoqual">
57 <param name="genoqual" type="integer" value="5" label="Set minimum mapping quality for genotyping" help="(--geno-qual)"/> 59 <param name="genoqual" type="integer" value="5" label="Set minimum mapping quality for genotyping" help="(--geno-qual)"/>
58 </xml> 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>
59 <xml name="minclip"> 70 <xml name="minclip">
60 <param argument="--minclip" type="integer" value="25" label="Set minimum clipping length"/> 71 <param argument="--minclip" type="integer" value="25" label="Set minimum clipping length"/>
61 </xml> 72 </xml>
62 <xml name="maxreadsep" token_default="40"> 73 <xml name="mincliquesize">
63 <param argument="--maxreadsep" type="integer" value="@DEFAULT@" label="Set maximum read separation"/> 74 <param name="mincliquesize" type="integer" value="2" label="Set minimum paired-end/single-read clique size" help="(--min-clique-size)"/>
64 </xml> 75 </xml>
65 <xml name="maxsize" token_default="1000000"> 76 <xml name="minrefsep" token_default="">
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"/> 77 <param argument="--minrefsep" type="integer" value="@DEFAULT@" label="Set minimum reference separation"/>
73 </xml> 78 </xml>
74 <xml name="minsize"> 79 <xml name="minsize" token_default="" token_label="">
75 <param argument="--minsize" type="integer" value="0" label="Set minimum SV size"/> 80 <param argument="--minsize" type="integer" value="@DEFAULT@" label="@LABEL@"/>
76 </xml> 81 </xml>
77 <xml name="samples" token_format="bam" token_multiple="true" token_label="Select sample file(s)"> 82 <xml name="pass">
78 <param name="samples" type="data" format="@FORMAT@" multiple="@MULTIPLE@" label="@LABEL@"/> 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."/>
79 </xml> 90 </xml>
80 <xml name="svtype"> 91 <xml name="svtype">
81 <param argument="--svtype" type="select" label="Select type(s) of structural variants to detect"> 92 <param argument="--svtype" type="select" label="Select type(s) of structural variants to detect">
82 <option value="ALL" selected="true">All types (ALL)</option> 93 <option value="ALL" selected="true">All types (ALL)</option>
83 <option value="DEL">Deletion (DEL)</option> 94 <option value="DEL">Deletion (DEL)</option>
95 <option value="DUP">Duplication (DUP)</option>
84 <option value="INS">Insertion (INS)</option> 96 <option value="INS">Insertion (INS)</option>
85 <option value="DUP">Duplication (DUP)</option>
86 <option value="INV">Inversion (INV)</option> 97 <option value="INV">Inversion (INV)</option>
87 <option value="BND">Translocation (BND)</option> 98 <option value="BND">Translocation (BND)</option>
88 </param> 99 </param>
89 </xml> 100 </xml>
90 <xml name="vcffile"> 101 <xml name="vcffile">
91 <param argument="--vcffile" type="data" format="vcf,bcf" optional="true" label="Select genotyping file"/> 102 <param argument="--vcffile" type="data" format="bcf,vcf" optional="true" label="Select genotyping file"/>
92 </xml> 103 </xml>
93 104
94 <!-- 105 <!-- output -->
95 output
96 -->
97 106
107 <xml name="bcf">
108 <data name="out_bcf" format="bcf" from_work_dir="result.bcf" label="${tool.name} on ${on_string}: Result (BCF)">
109 <filter>'bcf' in oo['out']</filter>
110 </data>
111 </xml>
98 <xml name="vcf"> 112 <xml name="vcf">
99 <data name="out_vcf" format="vcf" from_work_dir="result.vcf" label="${tool.name} on ${on_string}: Result (VCF)"> 113 <data name="out_vcf" format="vcf" from_work_dir="result.vcf" label="${tool.name} on ${on_string}: Result (VCF)">
100 <filter>'vcf' in oo['out']</filter> 114 <filter>'vcf' in oo['out']</filter>
101 </data>
102 </xml>
103 <xml name="bcf">
104 <data name="out_bcf" format="bcf" from_work_dir="result.bcf" label="${tool.name} on ${on_string}: Result (BCF)">
105 <filter>'bcf' in oo['out']</filter>
106 </data> 115 </data>
107 </xml> 116 </xml>
108 <xml name="dump"> 117 <xml name="dump">
109 <data name="out_dump" format="tabular" from_work_dir="dump.tsv" label="${tool.name} on ${on_string}: SV-reads"> 118 <data name="out_dump" format="tabular" from_work_dir="dump.tsv" label="${tool.name} on ${on_string}: SV-reads">
110 <filter>'dump' in oo['out']</filter> 119 <filter>'dump' in oo['out']</filter>
114 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log"> 123 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
115 <filter>'log' in oo['out']</filter> 124 <filter>'log' in oo['out']</filter>
116 </data> 125 </data>
117 </xml> 126 </xml>
118 127
119 <!-- 128 <!-- help -->
120 Help
121 -->
122 129
123 <token name="@WID@"><![CDATA[ 130 <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. 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
125 ]]></token> 147 ]]></token>
126 <token name="@REFERENCES@"><![CDATA[ 148 <token name="@REFERENCES@"><![CDATA[
127 More information are available on `GitHub <https://github.com/dellytools/delly>`_. 149 More information are available on `GitHub <https://github.com/dellytools/delly>`_.
128 ]]></token> 150 ]]></token>
129 </macros> 151 </macros>