Mercurial > repos > dfornika > mob_suite

diff mob_recon.xml @ 48:20dc7e1d2f4c draft

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"planemo upload for repository https://github.com/phac-nml/mob-suite commit d6d757cdcd6e012b1cfa9514b8b7157448a2c029-dirty"
author dfornika
date Wed, 11 Dec 2019 00:10:21 +0000
parents f286c91a0b92
children 4e818dfe0f23
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line diff
--- a/mob_recon.xml	Thu Nov 21 23:36:10 2019 +0000
+++ b/mob_recon.xml	Wed Dec 11 00:10:21 2019 +0000
@@ -1,17 +1,18 @@
-<tool id="mob_recon" name="MOB-Recon" version="2.0.2+galaxy0">
+<tool id="mob_recon" name="MOB-Recon" version="2.0.5+galaxy0">
   <description>Type contigs and extract plasmid sequences</description>
   <requirements>
-     <requirement type="package" version="2.0.2">mob_suite</requirement>
-  </requirements>   
+     <requirement type="package" version="2.0.5">mob_suite</requirement>
+  </requirements>
+  <version_command>mob_recon --version</version_command>
   <command detect_errors="exit_code">
   <![CDATA[  
     #import re
     #import os.path
     
-    #set $named_input = re.sub(r'(\s|\(|\)|:|!)', '_', str($input.element_identifier)+".fasta")
-    ln -s "$input" $named_input && 
+    #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}'
     #if str($adv_param.unicycler_contigs) == "True":
       --unicycler_contigs 
     #end if   
@@ -19,7 +20,7 @@
       --run_circlator 
     #end if 
     #if str($adv_param.min_length_condition.min_length_param) == "True":
-      --min_length ${adv_param.min_length_condition.min_length_value}
+      --min_length '${adv_param.min_length_condition.min_length_value}'
     #end if 
     --run_typer --min_rep_evalue '${adv_param.min_rep_evalue}'
     --min_rep_evalue '${adv_param.min_rep_evalue}'
@@ -68,7 +69,7 @@
     <data name="contig_report" format="tabular" from_work_dir="outdir/contig_report.txt" label="${tool.name} on ${on_string}: Overall contig MOB-recon report"/> 
     <data name="repetitive_blast_report" format="tabular" from_work_dir="outdir/repetitive_blast_report.txt" label="${tool.name} on ${on_string}: Repetitive elements BLAST report"/>
     <data name="mobtyper_aggregate_report" format="tabular" from_work_dir="outdir/mobtyper_aggregate_report.txt" label="${tool.name} on ${on_string}: Aggregate MOB-typer report for all contigs"/>
-    <data name="chromosome" format="fasta" from_work_dir="outdir/chromosome.fasta" label="${tool.name} on ${on_string}: Chromosome"/>
+    <data name="chromosome" format="fasta" from_work_dir="outdir/chromosome.fasta" label="${tool.name} on ${on_string}: Chromosomal sequences"/>
     <collection name="plasmids" type="list" label="${tool.name} on ${on_string}: Plasmids">
       <discover_datasets pattern="__name_and_ext__" directory="outdir/plasmids" />
     </collection>