Mercurial > repos > iuc > sansa_annotate

comparison macros.xml @ 0:608c3eefface 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/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
author iuc
date Mon, 25 Jan 2021 17:49:56 +0000
parents
children b4b8e88c6ff9
comparison
equal deleted inserted replaced
-1:000000000000 0:608c3eefface
1 <?xml version="1.0"?>
2 <macros>
3 <token name="@TOOL_VERSION@">0.0.7</token>
4 <token name="@VERSION_SUFFIX@">0</token>
5 <xml name="requirements">
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">sansa</requirement>
8 </requirements>
9 </xml>
10 <xml name="version_command">
11 <version_command><![CDATA[sansa -v | grep "Sansa " | cut -d "v" -f 3]]></version_command>
12 </xml>
13 <xml name="citations">
14 <citations>
15 <citation type="doi">10.1093/bioinformatics/bts378</citation>
16 </citations>
17 </xml>
18
19 <!-- input -->
20
21 <xml name="fg">
22 <section name="fg" title="Feature and gene annotation options" expanded="true">
23 <param argument="--gtf" type="data" format="gtf,gff3" label="Select file"/>
24 <param argument="--id" type="text" value="gene_name" label="Set GTF/GFF3 attribute">
25 <option value="exon_id">exon_id</option>
26 <option value="gene_id">gene_id</option>
27 <option value="gene_name">gene_name</option>
28 <option value="Name">Name</option>
29 </param>
30 <param argument="--feature" type="text" value="gene" label="Set GTF/GFF3 feature">
31 <option value="gene">gene</option>
32 <option value="exon">exon</option>
33 </param>
34 <param argument="--distance" type="integer" min="0" value="1000" label="Set maximum distance" help="0: overlapping features only"/>
35 </section>
36 </xml>
37 <xml name="s">
38 <section name="s" title="SV annotation options" expanded="true">
39 <param argument="--db" type="data" format="vcf,bcf" label="Select database file"/>
40 <param argument="--bpoffset" type="integer" value="50" label="Set maximum breakpoint offset"/>
41 <param argument="--ratio" type="float" min="0.0" max="1.0" value="0.8" label="Set minimum size ratio smaller SV to larger SV"/>
42 <param argument="--strategy" type="select" label="Select matching strategy">
43 <option value="best" selected="true">Best</option>
44 <option value="all">All</option>
45 </param>
46 <param argument="--notype" type="boolean" truevalue="-n" falsevalue="" label="Require matching SV types?"/>
47 <param argument="--nomatch" type="boolean" truevalue="-m" falsevalue="" label="Report SVs without match in database?"/>
48 </section>
49 </xml>
50 </macros>