Mercurial > repos > dfornika > artic_margin_cons_medaka

changeset 7:be08b76fd78b draft default tip

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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 22:05:59 +0000
parents f52f0a2778f8
children
files artic_margin_cons_medaka.xml
diffstat 1 files changed, 5 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/artic_margin_cons_medaka.xml	Tue Mar 17 21:42:53 2020 +0000
+++ b/artic_margin_cons_medaka.xml	Tue Mar 17 22:05:59 2020 +0000
@@ -6,14 +6,15 @@
         <requirement type="package" version="1.9">samtools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        ln -s '${input_alignment}' '${input_alignment.element_identifier}' &&
-        samtools index '${input_alignment.element_identifier}' &&
+        ln -s '${input_alignment}' '${input_alignment.element_identifier}.bam' &&
+        samtools index '${input_alignment.element_identifier}.bam' &&
+        ln -s '${input_variants}' '${input_variants.element_identifier}.vcf' &&
         python '${__tool_directory__}/margin_cons_medaka.py'
           --depth '${minimum_depth}'
           --quality '${minimum_quality}'
           '${ref_fasta}'
-          '${input_variants}'
-          '${input_alignment.element_identifier}'
+          '${input_variants.element_identifier}.vcf'
+          '${input_alignment.element_identifier}.bam'
           > '${consensus_fasta}'
           2> '${report}'
     ]]></command>