# HG changeset patch
# User dfornika
# Date 1579894306 0
# Node ID 774ebd2b0ed1c6be89b8e68cdd5071a06ebfa375
# Parent  7a048a2ed2e7f2c82542629095ced0eafcd6ba2d
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/chewbbaca commit 66a9f18802686a105b392e73e82c0078d0cdf2a4"

diff -r 7a048a2ed2e7 -r 774ebd2b0ed1 chewbbaca_allelecall.xml
--- a/chewbbaca_allelecall.xml	Fri Jan 24 17:43:33 2020 +0000
+++ b/chewbbaca_allelecall.xml	Fri Jan 24 19:31:46 2020 +0000
@@ -5,9 +5,10 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         chewBBACA.py AlleleCall
-          --threads \${GALAXY_SLOTS:-1}
+          --cpu \${GALAXY_SLOTS:-1}
           -i '${assembly}'
-          --bsr '${min_bsr}'
+          --ptf '${prodigal_training_file_source.prodigal_training_file.fields.path}'
+          --min_bsr ${min_bsr}
           --st '${size_threshold}'
         ]]>
     </command>
@@ -37,8 +38,6 @@
         <param name="min_bsr" type="float" value="0.6" optional="true" label="minimum BSR score" />
         <param name="size_threshold" type="float" min="0.0" value="0.2" max="1.0" optional="true" label="Size threshold" />
     </inputs>
-
-    <!-- define outputs -->
     <outputs>
         <data format="tabular" name="statistics" label="${tool.name}: on ${on_string}: Statistics" />
         <data format="tabular" name="contigs_info" label="${tool.name}: on ${on_string}: Contigs Info" />