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comparison macros.xml @ 1:c559b5bb484b draft

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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 20:48:16 +0000
parents 896c846866a6
children 445e356988a7
comparison
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0:896c846866a6 1:c559b5bb484b
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@TOOL_VERSION@">0.8.3</token> 3 <token name="@TOOL_VERSION@">0.8.5</token>
4 <token name="@DESCRIPTION@"></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>
9 </requirements> 9 </requirements>
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 <!--
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 <!--
21 input 47 input
22 --> 48 -->
23 49
24 <xml name="exclude"> 50 <xml name="exclude">
25 <param argument="--exclude" type="data" format="tabular" optional="true" label="Select file with regions to exclude"/> 51 <param argument="--exclude" type="data" format="tabular" optional="true" label="Select file with regions to exclude"/>
31 <param name="genoqual" type="integer" value="5" label="Set minimum mapping quality for genotyping" help="(--geno-qual)"/> 57 <param name="genoqual" type="integer" value="5" label="Set minimum mapping quality for genotyping" help="(--geno-qual)"/>
32 </xml> 58 </xml>
33 <xml name="minclip"> 59 <xml name="minclip">
34 <param argument="--minclip" type="integer" value="25" label="Set minimum clipping length"/> 60 <param argument="--minclip" type="integer" value="25" label="Set minimum clipping length"/>
35 </xml> 61 </xml>
36 <xml name="maxreadsep"> 62 <xml name="maxreadsep" token_default="40">
37 <param argument="--maxreadsep" type="integer" value="40" label="Set maximum read separation"/> 63 <param argument="--maxreadsep" type="integer" value="@DEFAULT@" label="Set maximum read separation"/>
38 </xml> 64 </xml>
39 <xml name="minrefsep"> 65 <xml name="maxsize" token_default="1000000">
40 <param argument="--minrefsep" type="integer" value="25" label="Set minimum reference separation"/> 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"/>
41 </xml> 76 </xml>
42 <xml name="samples" token_format="bam" token_multiple="true" token_label="Select sample file(s)"> 77 <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@"/> 78 <param name="samples" type="data" format="@FORMAT@" multiple="@MULTIPLE@" label="@LABEL@"/>
44 </xml> 79 </xml>
45 <xml name="svtype"> 80 <xml name="svtype">
74 <data name="out_dump" format="tabular" from_work_dir="dump.tsv" label="${tool.name} on ${on_string}: SV-reads"> 109 <data name="out_dump" format="tabular" from_work_dir="dump.tsv" label="${tool.name} on ${on_string}: SV-reads">
75 <filter>'dump' in oo['out']</filter> 110 <filter>'dump' in oo['out']</filter>
76 </data> 111 </data>
77 </xml> 112 </xml>
78 <xml name="log"> 113 <xml name="log">
79 <data name="out_log" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: Log"> 114 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
80 <filter>'log' in oo['out']</filter> 115 <filter>'log' in oo['out']</filter>
81 </data> 116 </data>
82 </xml> 117 </xml>
83 118
84 <!-- 119 <!--
87 122
88 <token name="@WID@"><![CDATA[ 123 <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. 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.
90 ]]></token> 125 ]]></token>
91 <token name="@REFERENCES@"><![CDATA[ 126 <token name="@REFERENCES@"><![CDATA[
92 More information are available on `github <https://github.com/dellytools/delly>`_. 127 More information are available on `GitHub <https://github.com/dellytools/delly>`_.
93 ]]></token> 128 ]]></token>
94 </macros> 129 </macros>