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planemo upload for repository https://github.com/galaxyproject/tools-iuc/vcfanno/ commit b1be52deee49703c602af519df3515e6ae957167
author iuc
date Sun, 25 Feb 2024 18:11:24 +0000
parents cdcaa40e5e45
children
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1 <?xml version="1.0"?>
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2 <macros>
2
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3 <token name="@TOOL_VERSION@">0.3.5</token>
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4 <token name="@VERSION_SUFFIX@">0</token>
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5 <token name="@PROFILE@">20.01</token>
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6 <xml name="requirements">
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">vcfanno</requirement>
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9 <requirement type="package" version="1.11">tabix</requirement>
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10 <requirement type="package" version="1.19.2">samtools</requirement>
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11 </requirements>
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12 </xml>
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13 <xml name="version_command">
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14 <version_command>vcfanno --help</version_command>
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15 </xml>
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16 <xml name="citations">
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17 <citations>
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18 <citation type="bibtex">@online{vcfanno,
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19 author = {Brent S. Pedersen},
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20 title = {vcfanno},
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21 year = 2016,
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22 url = {https://github.com/brentp/vcfanno},
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23 urldate = {2020-12-03}
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24 }</citation>
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25 <citation type="doi">10.1186/s13059-016-0973-5</citation>
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26 </citations>
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27 </xml>
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28 <xml name="xrefs">
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29 <xrefs>
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30 <xref type="bio.tools">vcfanno</xref>
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31 </xrefs>
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32 </xml>
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33
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34 <!--
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35 Inputs
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36 -->
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37 <macro name = "ops">
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38 <option value="self" selected="true">self - pull directly from the annotation and handle multi-allelics</option>
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39 <option value="concat">concat - comma delimited list of output</option>
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40 <option value="count">count - count the number of overlaps</option>
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41 <option value="div2">div2 - given two values a and b, return a / b</option>
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42 <option value="first">first - take only the first value</option>
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43 <option value="flag">flag - presense/absence via VCF flag</option>
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44 <option value="max">max (numbers only)</option>
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45 <option value="mean">mean (numbers only)</option>
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46 <option value="min">min (numbers only)</option>
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47 <option value="sum">sum (numbers only)</option>
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48 <option value="uniq">uniq - comma-delimited list of uniq values</option>
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49 <option value="by_alt">by_alt - comma-delimited by alt (Number=A), pipe-delimited (|) for multiple annos for the same alt.</option>
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50 <yield/>
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51 </macro>
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52
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53 <!--
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54 Help
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55 -->
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56
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57 <token name="@WID@"><![CDATA[
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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.
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59
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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.
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61
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62 - For BED, values are pulled from (1-based) column number.
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63
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64 - For BAM, depth (count), "mapq" and "seq" are currently supported.
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65 ]]></token>
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66 <token name="@REFERENCES@"><![CDATA[
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67 More information are available in the `mailing list <https://groups.google.com/g/vcfanno>`_ and `github <https://github.com/brentp/vcfanno>`_.
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68 ]]></token>
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69 </macros>