diff get_hrun.xml @ 0:84f70ce0b830 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_hrun.xml	Tue Mar 02 21:35:40 2021 +0000
@@ -0,0 +1,41 @@
+<?xml version="1.0"?>
+<tool id="get_hrun" name="Get homopolymer run length" version="@VERSION@+galaxy0" profile="@PROFILE@" license="MIT">
+    <description>Annotate indel variants with homopolymer context</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '${reference}' ref.fa &&
+        samtools faidx ref.fa &&
+        python '${__tool_directory__}/get_hrun.py' --reference ref.fa --in-vcf '${in_vcf}' --out-vcf '${out_vcf}'
+]]></command>
+    <inputs>
+        <param argument="--in-vcf" type="data" format="vcf" label="Input VCF"/>
+        <param argument="--reference" type="data" format="fasta" label="Input Reference FASTA"/>
+    </inputs>
+    <outputs>
+        <data name="out_vcf" format="vcf" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="in_vcf" value="in.vcf"/>
+            <param name="reference" value="reference.fasta"/>
+            <output name="out_vcf" value="out.vcf"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+@WID@
+
+**Inputs**
+- VCF file
+- Reference file for that VCF
+**Outputs**
+- VCF with annotated homopolymers
+]]></help>
+    <expand macro="citations"/>
+</tool>