diff vardict.xml @ 3:e0734e88a104 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 80e3742f499e8efabad1fe7627201466d0bdd190"

--- a/vardict.xml	Tue Nov 16 19:05:56 2021 +0000
+++ b/vardict.xml	Thu Jan 27 15:19:23 2022 +0000
@@ -4,6 +4,7 @@
         <import>macros.xml</import>
     </macros>
     <requirements>
+        <requirement type="package" version="3.10.2">python</requirement>
         <requirement type="package" version="@TOOL_VERSION@">vardict-java</requirement>
         <requirement type="package" version="5.1.0">gawk</requirement>
         <requirement type="package" version="1.14">samtools</requirement>
@@ -32,7 +33,7 @@
         #else
             ln -s ./ref.fa.fai ./chromosomes.fa.fai &&
         #end if
-        awk 'BEGIN {FS=OFS="\t"} {print $1, "1", $2}' ./chromosomes.fa.fai > ./regions.bed &&
+        python '$__tool_directory__/split.py' ./chromosomes.fa.fai "\${VARDICT_CHUNKSIZE:-1000000}" "\${VARDICT_OVERLAP:-150}" > ./regions.bed &&
 
         vardict-java
         #if $select_mode.mode == "paired"
@@ -128,6 +129,7 @@
                 <param name="reference_source_selector" value="history"/>
                 <param name="ref_file" ftype="fasta" value="genome.fasta" />
             </conditional>
+
             <output name="all_variants" compare="re_match_multiline" file="all_variants_paired.vcf" />
             <output name="passed_variants" compare="re_match_multiline" file="passed_variants_paired.vcf" />
         </test>
@@ -141,6 +143,7 @@
                 <param name="reference_source_selector" value="cached"/>
                 <param name="ref_file" value="test_buildid"/>
             </conditional>
+
             <output name="all_variants" compare="re_match_multiline" file="all_variants_paired.vcf" />
             <output name="passed_variants" compare="re_match_multiline" file="passed_variants_paired.vcf" />
         </test>