diff macros.xml @ 0:fb20fa735dfe draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/vcfanno/ commit d962b44c5d3fecd1a315d6fbda8831d6de1b2801"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Jan 21 10:33:49 2021 +0000
@@ -0,0 +1,69 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@TOOL_VERSION@">0.3.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">20.01</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">vcfanno</requirement>
+            <requirement type="package">tabix</requirement>
+            <requirement type="package">samtools</requirement>
+        </requirements>
+    </xml>
+    <xml name="version_command">
+        <version_command>vcfanno --help</version_command>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">@online{vcfanno,
+              author = {Brent S. Pedersen},
+              title = {vcfanno},
+              year = 2016,
+              url = {https://github.com/brentp/vcfanno},
+              urldate = {2020-12-03}
+            }</citation>
+            <citation type="doi">10.1186/s13059-016-0973-5</citation>
+        </citations>
+    </xml>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">vcfanno</xref>
+        </xrefs>
+    </xml>
+
+    <!--
+        Inputs
+    -->
+    <macro name = "ops">
+        <option value="self" selected="true">self - pull directly from the annotation and handle multi-allelics</option>
+        <option value="concat">concat - comma delimited list of output</option>
+        <option value="count">count - count the number of overlaps</option>
+        <option value="div2">div2 - given two values a and b, return a / b</option>
+        <option value="first">first - take only the first value</option>
+        <option value="flag">flag - presense/absence via VCF flag</option>
+        <option value="max">max (numbers only)</option>
+        <option value="mean">mean (numbers only)</option>
+        <option value="min">min (numbers only)</option>
+        <option value="sum">sum (numbers only)</option>
+        <option value="uniq">uniq - comma-delimited list of uniq values</option>
+        <option value="by_alt">by_alt - comma-delimited by alt (Number=A), pipe-delimited (|) for multiple annos for the same alt.</option>
+        <yield/>
+    </macro>
+
+    <!--
+        Help
+    -->
+
+    <token name="@WID@"><![CDATA[
+*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.
+
+ - For VCF, values are pulled by name from the INFO field with special-cases of ID and FILTER to pull from those VCF columns.
+ 
+ - For BED, values are pulled from (1-based) column number.
+ 
+ - For BAM, depth (count), "mapq" and "seq" are currently supported.
+ ]]></token>
+    <token name="@REFERENCES@"><![CDATA[
+More information are available in the `mailing list <https://groups.google.com/g/vcfanno>`_ and `github <https://github.com/brentp/vcfanno>`_.
+    ]]></token>
+</macros>