Mercurial > repos > dfornika > artic_margin_cons_medaka

diff artic_margin_cons_medaka.xml @ 5:47eb99e41bfb draft

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_margin_cons_medaka commit cdc887baab41af2b386b1ec7239b55d474c0fff5-dirty"
author dfornika
date Tue, 17 Mar 2020 21:20:38 +0000
parents eb4af87a77ff
children f52f0a2778f8
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line diff
--- a/artic_margin_cons_medaka.xml	Wed Mar 11 02:31:04 2020 +0000
+++ b/artic_margin_cons_medaka.xml	Tue Mar 17 21:20:38 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="artic_margin_cons_medaka" name="ARTIC margin_cons_medaka" version="0.1.0+galaxy0">
+<tool id="artic_margin_cons_medaka" name="ARTIC margin_cons_medaka" version="0.1.0-1005a47+galaxy0">
     <description>Generate consensus fasta file from a reference fasta, bam alignment and VCF file</description>
     <requirements>
         <requirement type="package" version="0.6.8">pyvcf</requirement>
@@ -6,14 +6,14 @@
         <requirement type="package" version="1.9">samtools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        ln -s '${input_alignment}' alignment.bam &&
-        samtools index alignment.bam &&
+        ln -s '${input_alignment}' '${input_alignment.element_identifier}' alignment.bam &&
+        samtools index '${input_alignment.element_identifier}' &&
         python '${__tool_directory__}/margin_cons_medaka.py'
           --depth '${minimum_depth}'
           --quality '${minimum_quality}'
           '${ref_fasta}'
           '${input_variants}'
-          alignment.bam
+          '${input_alignment.element_identifier}'
           > '${consensus_fasta}'
           2> '${report}'
     ]]></command>