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comparison macros.xml @ 0:c5ce2f4ecefd draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/vcfanno/ commit d962b44c5d3fecd1a315d6fbda8831d6de1b2801"
author iuc
date Thu, 21 Jan 2021 10:33:23 +0000
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children 166af50b0a8d
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-1:000000000000 0:c5ce2f4ecefd
1 <?xml version="1.0"?>
2 <macros>
3 <token name="@TOOL_VERSION@">0.3.2</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@">vcfanno</requirement>
9 <requirement type="package">tabix</requirement>
10 <requirement type="package">samtools</requirement>
11 </requirements>
12 </xml>
13 <xml name="version_command">
14 <version_command>vcfanno --help</version_command>
15 </xml>
16 <xml name="citations">
17 <citations>
18 <citation type="bibtex">@online{vcfanno,
19 author = {Brent S. Pedersen},
20 title = {vcfanno},
21 year = 2016,
22 url = {https://github.com/brentp/vcfanno},
23 urldate = {2020-12-03}
24 }</citation>
25 <citation type="doi">10.1186/s13059-016-0973-5</citation>
26 </citations>
27 </xml>
28 <xml name="xrefs">
29 <xrefs>
30 <xref type="bio.tools">vcfanno</xref>
31 </xrefs>
32 </xml>
33
34 <!--
35 Inputs
36 -->
37 <macro name = "ops">
38 <option value="self" selected="true">self - pull directly from the annotation and handle multi-allelics</option>
39 <option value="concat">concat - comma delimited list of output</option>
40 <option value="count">count - count the number of overlaps</option>
41 <option value="div2">div2 - given two values a and b, return a / b</option>
42 <option value="first">first - take only the first value</option>
43 <option value="flag">flag - presense/absence via VCF flag</option>
44 <option value="max">max (numbers only)</option>
45 <option value="mean">mean (numbers only)</option>
46 <option value="min">min (numbers only)</option>
47 <option value="sum">sum (numbers only)</option>
48 <option value="uniq">uniq - comma-delimited list of uniq values</option>
49 <option value="by_alt">by_alt - comma-delimited by alt (Number=A), pipe-delimited (|) for multiple annos for the same alt.</option>
50 <yield/>
51 </macro>
52
53 <!--
54 Help
55 -->
56
57 <token name="@WID@"><![CDATA[
58 *vcfanno* allows you to quickly annotate your VCF with any number of INFO fields from any number of VCFs or BED files. It uses a simple conf file to allow the user to specify the source annotation files and fields and how they will be added to the info of the query VCF.
59
60 - For VCF, values are pulled by name from the INFO field with special-cases of ID and FILTER to pull from those VCF columns.
61
62 - For BED, values are pulled from (1-based) column number.
63
64 - For BAM, depth (count), "mapq" and "seq" are currently supported.
65 ]]></token>
66 <token name="@REFERENCES@"><![CDATA[
67 More information are available in the `mailing list <https://groups.google.com/g/vcfanno>`_ and `github <https://github.com/brentp/vcfanno>`_.
68 ]]></token>
69 </macros>