Mercurial > repos > iuc > delly_call

annotate macros.xml @ 1:53d90d86fc83 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
author iuc
date Thu, 29 Oct 2020 20:50:39 +0000
parents 36772204dee5
children 9946bd542898
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
2 <macros>
1
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
3 <token name="@TOOL_VERSION@">0.8.5</token>
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
4 <token name="@VERSION_SUFFIX@">0</token>
0
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
5 <xml name="requirements">
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
6 <requirements>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
7 <requirement type="package" version="@TOOL_VERSION@">delly</requirement>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
8 <requirement type="package" version="1.10.2">bcftools</requirement>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
9 </requirements>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
10 </xml>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
11 <xml name="version_command">
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
12 <version_command><![CDATA[delly -v 2>&1 | grep 'Delly version' | cut -f 3 -d ' ']]></version_command>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
13 </xml>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
14 <xml name="citations">
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
15 <citations>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
16 <citation type="doi">10.1093/bioinformatics/bts378</citation>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
17 </citations>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
18 </xml>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
19
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
20 <!--
1
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
21 command
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
22 -->
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
23
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
24 <token name="@BAM@"><![CDATA[
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
25 #for $i, $current in enumerate($samples)
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
26 ln -s '${current}' 'sample_${i}.bam' &&
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
27 ln -s '${current.metadata.bam_index}' 'sample_${i}.bam.bai' &&
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
28 #end for
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
29 ]]></token>
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
30 <token name="@DUMP@"><![CDATA[
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
31 #if 'dump' in $oo.out
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
32 && test -f 'dump.tsv.gz' && bgzip -d 'dump.tsv.gz' || echo 'No dump file.'
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
33 #end if
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
34 ]]></token>
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
35 <token name="@LOG@"><![CDATA[
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
36 #if 'log' in $oo.out
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
37 |& tee '$out_log'
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
38 #end if
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
39 ]]></token>
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
40 <token name="@VCF@"><![CDATA[
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
41 #if 'vcf' in $oo.out
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
42 && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.'
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
43 #end if
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
44 ]]></token>
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
45
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
46 <!--
0
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
47 input
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
48 -->
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
49
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
50 <xml name="exclude">
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
51 <param argument="--exclude" type="data" format="tabular" optional="true" label="Select file with regions to exclude"/>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
52 </xml>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
53 <xml name="genome">
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
54 <param argument="--genome" type="data" format="fasta" label="Select genome"/>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
55 </xml>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
56 <xml name="genoqual">
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
57 <param name="genoqual" type="integer" value="5" label="Set minimum mapping quality for genotyping" help="(--geno-qual)"/>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
58 </xml>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
59 <xml name="minclip">
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
60 <param argument="--minclip" type="integer" value="25" label="Set minimum clipping length"/>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
61 </xml>
1
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
62 <xml name="maxreadsep" token_default="40">
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
63 <param argument="--maxreadsep" type="integer" value="@DEFAULT@" label="Set maximum read separation"/>
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
64 </xml>
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
65 <xml name="maxsize" token_default="1000000">
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
66 <param argument="--maxsize" type="integer" value="@DEFAULT@" label="Set maximum SV size"/>
0
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
67 </xml>
1
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
68 <xml name="mincliquesize">
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
69 <param name="mincliquesize" type="integer" value="2" label="Set minimum min. PE/SR clique size" help="(--min-clique-size)"/>
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
70 </xml>
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
71 <xml name="minrefsep" token_default="25">
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
72 <param argument="--minrefsep" type="integer" value="@DEFAULT@" label="Set minimum reference separation"/>
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
73 </xml>
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
74 <xml name="minsize">
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
75 <param argument="--minsize" type="integer" value="0" label="Set minimum SV size"/>
0
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
76 </xml>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
77 <xml name="samples" token_format="bam" token_multiple="true" token_label="Select sample file(s)">
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
78 <param name="samples" type="data" format="@FORMAT@" multiple="@MULTIPLE@" label="@LABEL@"/>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
79 </xml>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
80 <xml name="svtype">
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
81 <param argument="--svtype" type="select" label="Select type(s) of structural variants to detect">
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
82 <option value="ALL" selected="true">All types (ALL)</option>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
83 <option value="DEL">Deletion (DEL)</option>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
84 <option value="INS">Insertion (INS)</option>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
85 <option value="DUP">Duplication (DUP)</option>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
86 <option value="INV">Inversion (INV)</option>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
87 <option value="BND">Translocation (BND)</option>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
88 </param>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
89 </xml>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
90 <xml name="vcffile">
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
91 <param argument="--vcffile" type="data" format="vcf,bcf" optional="true" label="Select genotyping file"/>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
92 </xml>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
93
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
94 <!--
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
95 output
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
96 -->
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
97
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
98 <xml name="vcf">
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
99 <data name="out_vcf" format="vcf" from_work_dir="result.vcf" label="${tool.name} on ${on_string}: Result (VCF)">
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
100 <filter>'vcf' in oo['out']</filter>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
101 </data>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
102 </xml>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
103 <xml name="bcf">
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
104 <data name="out_bcf" format="bcf" from_work_dir="result.bcf" label="${tool.name} on ${on_string}: Result (BCF)">
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
105 <filter>'bcf' in oo['out']</filter>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
106 </data>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
107 </xml>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
108 <xml name="dump">
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
109 <data name="out_dump" format="tabular" from_work_dir="dump.tsv" label="${tool.name} on ${on_string}: SV-reads">
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
110 <filter>'dump' in oo['out']</filter>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
111 </data>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
112 </xml>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
113 <xml name="log">
1
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
114 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
0
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
115 <filter>'log' in oo['out']</filter>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
116 </data>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
117 </xml>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
118
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
119 <!--
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
120 Help
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
121 -->
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
122
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
123 <token name="@WID@"><![CDATA[
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
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.
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
125 ]]></token>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
126 <token name="@REFERENCES@"><![CDATA[
1
53d90d86fc83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
parents: 0
diff changeset
127 More information are available on `GitHub <https://github.com/dellytools/delly>`_.
0
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
128 ]]></token>
36772204dee5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
iuc
parents:
diff changeset
129 </macros>