# HG changeset patch
# User dfornika
# Date 1583892885 0
# Node ID 24c5caa214e732fb90eccf01f6a02ad97fb40d7f
# Parent  9fcffca8f6ad4c66ed242f0150882460cba6d993
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit c866a76470b72bf5abdc2a88e6bf584c2f2f9b02-dirty"

diff -r 9fcffca8f6ad -r 24c5caa214e7 artic_margin_cons_medaka.xml
--- a/artic_margin_cons_medaka.xml	Wed Mar 11 02:00:01 2020 +0000
+++ b/artic_margin_cons_medaka.xml	Wed Mar 11 02:14:45 2020 +0000
@@ -3,14 +3,17 @@
     <requirements>
         <requirement type="package" version="0.6.8">pyvcf</requirement>
         <requirement type="package" version="1.76">biopython</requirement>
+        <requirement type="package" version="1.9">samtools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+        ln -s '${input_alignment}' alignment.bam &&
+        samtools index alignment.bam &&
         python '${__tool_directory__}/margin_cons_medaka.py'
           --depth '${minimum_depth}'
           --quality '${minimum_quality}'
           '${ref_fasta}'
           '${input_variants}'
-          '${input_alignment}'
+          alignment.bam
           > '${consensus_fasta}'
           2> '${report}'
     ]]></command>
@@ -23,7 +26,7 @@
     </inputs>
     <outputs>
         <data name="consensus_fasta" format="fasta" label="${tool.name} on ${on_string}: Consensus (.fasta)" />
-        <data name="report" format="tabular" label="${tool.name} on ${on_string}: Report" />
+        <data name="report" format="txt" label="${tool.name} on ${on_string}: Report" />
     </outputs>
     <tests>
     </tests>