Mercurial > repos > iuc > sansa_annotate

diff macros.xml @ 0:fb00426402b0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
author iuc
date Mon, 25 Jan 2021 17:50:47 +0000
parents
children e3862632706d
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Jan 25 17:50:47 2021 +0000
@@ -0,0 +1,50 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@TOOL_VERSION@">0.0.7</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">sansa</requirement>
+        </requirements>
+    </xml>
+    <xml name="version_command">
+        <version_command><![CDATA[sansa -v | grep "Sansa " | cut -d "v" -f 3]]></version_command>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/bioinformatics/bts378</citation>
+        </citations>
+    </xml>
+
+    <!-- input -->
+
+    <xml name="fg">
+        <section name="fg" title="Feature and gene annotation options" expanded="true">
+            <param argument="--gtf" type="data" format="gtf,gff3" label="Select file"/>
+            <param argument="--id" type="text" value="gene_name" label="Set GTF/GFF3 attribute">
+                <option value="exon_id">exon_id</option>
+                <option value="gene_id">gene_id</option>
+                <option value="gene_name">gene_name</option>
+                <option value="Name">Name</option>
+            </param>
+            <param argument="--feature" type="text" value="gene" label="Set GTF/GFF3 feature">
+                <option value="gene">gene</option>
+                <option value="exon">exon</option>
+            </param>
+            <param argument="--distance" type="integer" min="0" value="1000" label="Set maximum distance" help="0: overlapping features only"/>
+        </section>
+    </xml>
+    <xml name="s">
+        <section name="s" title="SV annotation options" expanded="true">
+            <param argument="--db" type="data" format="vcf,bcf" label="Select database file"/>
+            <param argument="--bpoffset" type="integer" value="50" label="Set maximum breakpoint offset"/>
+            <param argument="--ratio" type="float" min="0.0" max="1.0" value="0.8" label="Set minimum size ratio smaller SV to larger SV"/>
+            <param argument="--strategy" type="select" label="Select matching strategy">
+                <option value="best" selected="true">Best</option>
+                <option value="all">All</option>
+            </param>
+            <param argument="--notype" type="boolean" truevalue="-n" falsevalue="" label="Require matching SV types?"/>
+            <param argument="--nomatch" type="boolean" truevalue="-m" falsevalue="" label="Report SVs without match in database?"/>
+        </section>
+    </xml>
+</macros>