# HG changeset patch
# User iuc
# Date 1656328900 0
# Node ID 4c52b134a42f945a48622d03016e263ece0ad06e
# Parent  96bf82df80c6f029022970843974f134ac5854ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit ab4afb50e6c991cc2e784a93a0c7a75329eac88c

diff -r 96bf82df80c6 -r 4c52b134a42f fermikit_run_calling.xml
--- a/fermikit_run_calling.xml	Thu Jan 05 08:35:17 2017 -0500
+++ b/fermikit_run_calling.xml	Mon Jun 27 11:21:40 2022 +0000
@@ -1,13 +1,23 @@
-<tool id="fermikit_variants" name="fermikit-variants" version="0.14.dev1">
+<tool id="fermikit_variants" name="fermikit-variants" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>call variants from genome-aligned contigs</description>
+    <macros>
+        <token name="@TOOL_VERSION@">0.14.dev1</token>
+        <token name="@VERSION_SUFFIX@">1</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="0.14.dev1">fermikit</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">fermikit</requirement>
         <requirement type="package" version="0.6.5">sambamba</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         #import re
         #set escaped_element_identifier = re.sub('[^\w\-\s]', '_', str($bam.element_identifier))
-        #set ref = $reference_genome.fasta_item.fields.path if $reference_genome.reference_genome_source == "reference" else $reference_genome.history_item
+        
+        #if $reference_genome.reference_genome_source == "reference"
+            #set ref=$reference_genome.fasta_item.fields.path
+        #else
+            ln -s '$reference_genome.history_item' reference.fa &&
+            #set ref="reference.fa"
+        #end if        
         export ROOT=\$(dirname \$(type -P k8)) &&
         ln -f -s '$bam' '$escaped_element_identifier' &&
         htsbox pileup -cuf '$ref' '$escaped_element_identifier'  | gzip -1 > raw.vcf.gz &&