Mercurial > repos > estrain > microrunqc

diff microrunqc.xml @ 13:59e137488c63 draft

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Uploaded
author estrain
date Wed, 24 May 2023 17:24:23 +0000
parents 50867379763d
children c3eb197a283b
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line diff
--- a/microrunqc.xml	Fri Mar 10 17:01:21 2023 +0000
+++ b/microrunqc.xml	Wed May 24 17:24:23 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="microrunqc" name="microrunqc" version="1.0.0">
+<tool id="microrunqc" name="microrunqc" version="1.0.1">
 
   <requirements>
     <requirement type="package" version="2.4.0">skesa</requirement>
@@ -103,7 +103,9 @@
         --minscore $options.minscore
       #end if
     #end if
-    ${outname}.fasta > ${outname}.mlst.tsv;
+    ${outname}.fasta > ${outname}.mlst_raw.tsv;
+    
+    perl mlstAddFields.pl ${outname}.mlst_raw.tsv > ${outname}.mlst.tsv;
 
     python $__tool_directory__/run_fastq_scan.py --fastq ${bwalist} --out fq_out.tab --type ${fqscan};