Mercurial > repos > dfornika > mob_suite

changeset 1:40cb4eecef7c draft

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planemo upload for repository https://github.com/phac-nml/mob-suite commit 4c922d083dff667315e2ba083bbb070c019ba694-dirty
author dfornika
date Fri, 21 Jun 2019 20:55:59 -0400
parents 9ff41cda745f
children 31057f26bbb8
files mob_recon.xml
diffstat 1 files changed, 9 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/mob_recon.xml	Fri Jun 21 20:47:15 2019 -0400
+++ b/mob_recon.xml	Fri Jun 21 20:55:59 2019 -0400
@@ -11,7 +11,10 @@
     #set $named_input = re.sub(r'(\s|\(|\)|:|!)', '_', str($input.element_identifier)+".fasta")
     ln -s "$input" $named_input && 
     
-    mob_recon  --num_threads \${GALAXY_SLOTS:-4}  --infile "${named_input}" 
+    mob_recon  
+      --num_threads \${GALAXY_SLOTS:-4}  
+      --infile "${named_input}" 
+      --database-directory '${mob_suite_database_dir}'
     #if str($adv_param.unicycler_contigs) == "True":
       --unicycler_contigs 
     #end if   
@@ -35,6 +38,11 @@
   </command>
   <inputs>
     <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
+    <param name="mob_suite_database_dir" type="select">
+      <options from_data_table="mob_suite_databases">
+	<validator type="no_options" message="No MOB-Suite databases are available" />
+      </options>
+    </param>
     <section name="adv_param" title="Advanced parameters" expanded="False">
       <param name="unicycler_contigs" label="Check for circularity flag generated by unicycler in contigs fasta headers" type="select" value="True">
         <option value="True">Yes</option>