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comparison macros.xml @ 0:630e2929a131 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/jasminesv/ commit eb5baa10589b31c422ec8b8980617a3f375608ad"
author iuc
date Wed, 20 Jan 2021 19:49:40 +0000
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children 2b62154e39c8
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-1:000000000000 0:630e2929a131
1 <?xml version="1.0"?>
2 <macros>
3 <token name="@TOOL_VERSION@">1.0.11</token>
4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@PROFILE@">20.01</token>
6 <xml name="requirements">
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">jasminesv</requirement>
9 </requirements>
10 </xml>
11 <xml name="version_command">
12 <version_command>jasmine</version_command>
13 </xml>
14 <xml name="citations">
15 <citations>
16 <citation type="bibtex">@online{jasmine,
17 author = {Melanie Kirsche},
18 title = {jasmine},
19 year = 2021,
20 url = {https://github.com/mkirsche/Jasmine},
21 urldate = {2021-01-13}
22 }</citation>
23 </citations>
24 </xml>
25 <!--
26 Command
27 -->
28 <token name="@REF_FASTA@"><![CDATA[
29 #if $dup_to_ins.reference_source.reference_source_selector == 'history':
30 ln -f -s '$dup_to_ins.reference_source.ref_file' reference.fa &&
31 #else:
32 ln -f -s '$dup_to_ins.reference_source.ref_file.fields.path' reference.fa &&
33 #end if
34 ]]></token>
35
36 <xml name="reference">
37 <conditional name="reference_source">
38 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
39 <option value="cached">Use a built-in genome</option>
40 <option value="history">Use a genome from history</option>
41 </param>
42 <when value="cached">
43 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
44 <options from_data_table="all_fasta">
45 <filter type="sort_by" column="2"/>
46 <validator type="no_options" message="No reference genomes are available"/>
47 </options>
48 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
49 </param>
50 </when>
51 <when value="history">
52 <param name="ref_file" type="data" format="fasta,fastq" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference"/>
53 </when>
54 </conditional>
55 </xml>
56 <!--
57 Help
58 -->
59
60 <token name="@WID@"><![CDATA[
61 *Jasmine*, or Jointly Accurate Sv Merging with Intersample Network Edges is a tool used to merge structural variants (SVs) across samples. Each sample has a number of SV calls, consisting of position information (chromosome, start, end, length), type and strand information, and a number of other values. Jasmine represents the set of all SVs across samples as a network, and uses a modified minimum spanning forest algorithm to determine the best way of merging the variants such that each merged variants represents a set of analogous variants occurring in different samples.
62 ]]></token>
63 <token name="@REFERENCES@"><![CDATA[
64 More information is available in the `github <https://github.com/mkirsche/Jasmine>`_.
65 ]]></token>
66 </macros>