Mercurial > repos > estrain > microrunqc

changeset 16:b07d5fec5942 draft

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Uploaded
author estrain
date Thu, 18 Jan 2024 20:14:55 +0000
parents c3eb197a283b
children ae1d6750b4db
files microrunqc.xml
diffstat 1 files changed, 9 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/microrunqc.xml	Wed May 24 17:57:57 2023 +0000
+++ b/microrunqc.xml	Thu Jan 18 20:14:55 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="microrunqc" name="microrunqc" version="1.0.1">
+<tool id="microrunqc" name="microrunqc" version="1.0.2">
 
   <requirements>
     <requirement type="package" version="2.4.0">skesa</requirement>
@@ -91,7 +91,7 @@
     bwa index ${outname}.fasta;
     bwa mem -t $num_cores  ${outname}.fasta ${bwalist} | python $__tool_directory__/median_size.py > insert.median;
  
-    mlst --nopath --threads $num_cores 
+    mlst --nopath --threads $num_cores --datadir $mlst_databases.fields.path/pubmlst --blastdb $mlst_databases.fields.path/blast/mlst.fa  
     #if $options.select=="advanced"
       #if $options.minid
         --minid $options.minid
@@ -158,6 +158,13 @@
         </when>
         <when value="basic"/>
       </conditional>
+
+      <param name="mlst_databases" label="Select a mlst database" type="select">
+          <options from_data_table="mlst">
+              <validator message="No database is available" type="no_options" />
+          </options>
+      </param>
+
     </inputs>
     <outputs>
       <data format="fasta" name="results.skesa.fasta" label="${tool.name} on ${on_string}: Contigs" from_work_dir="*.fasta"/>