# HG changeset patch
# User thanhlv
# Date 1568209888 14400
# Node ID a9e5d593228e7ea72093d9c53bd72d915b9a0344
# Parent  f92ab7729a35e5b0df38cf781829d69006e68aab
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/ncbi-armfinderplus commit 2c3091cc8850849ac99884f92f195e4de9774f99

diff -r f92ab7729a35 -r a9e5d593228e amrfinderplus.xml
--- a/amrfinderplus.xml	Tue Sep 10 12:32:19 2019 -0400
+++ b/amrfinderplus.xml	Wed Sep 11 09:51:28 2019 -0400
@@ -29,7 +29,7 @@
             -g '$input_selection.gff.gff_file'
         #end if
     #end if
-    #if str($organism) != 'none'
+    #if str($organism) != 'None'
         -O $organism
     #end if
     -o results.tsv
@@ -87,7 +87,6 @@
             </options>
         </param>
         <param name="organism" type="select" optional="true" label="Get organism-specific results">
-            <option value="none" selected="true">None</option>
             <option value="Campylobacter">Campylobacter</option>
             <option value="Escherichia">Escherichia</option>
             <option value="Klebsiella">Klebsiella</option>
@@ -112,13 +111,13 @@
 
     <tests>
         <test> <!-- dna input-->
-            <param name="input_selection|input_source_selector" value="nuc"/>
+            <param name="input_source_selector" value="nuc"/>
             <param name="fasta_file" value="test_dna.fa" ftype="fasta"/>
             <param name="amrfinder_databases" value="2019-08-27.1" />
             <output name="result" file="test_dna.expected" lines_diff="1"/>
         </test>
         <test> <!-- dna input and organism, plus gene-->
-            <param name="input_selection|input_source_selector" value="nuc"/>
+            <param name="input_source_selector" value="nuc"/>
             <param name="fasta_file" value="test_dna.fa" ftype="fasta"/>
             <param name="organism" value="Escherichia" />
             <param name="plus" value="true" />
@@ -126,17 +125,17 @@
             <output name="result" file="test_dna_Escherichia.expected" lines_diff="1"/>
         </test>
         <test> <!-- AA input-->
-            <param name="input_selection|input_source_selector" value="pro"/>
+            <param name="input_source_selector" value="pro"/>
             <param name="fasta_file" value="test_prot.fa" ftype="fasta"/>
             <param name="amrfinder_databases" value="2019-08-27.1" />
             <output name="result" file="test_prot.expected" lines_diff="1"/>
         </test>
         <test> <!-- DNA and AA input-->
-            <param name="input_selection|input_source_selector" value="both"/>
-            <param name="input_selection|input_source_selector|gff|use" value="gff_yes"/>
+            <param name="input_source_selector" value="both"/>
+            <param name="use" value="gff_yes"/>
             <param name="nuc_file" value="test_dna.fa" ftype="fasta"/>
             <param name="pro_file" value="test_prot.fa" ftype="fasta"/>
-            <param name="input_selection|gff|use" value="gff_yes"/>
+            <param name="use" value="gff_yes"/>
             <param name="gff_file" value="test_prot.gff" ftype="gff3"/>
             <param name="amrfinder_databases" value="2019-08-27.1" />
             <output name="result" file="test_both.expected" lines_diff="1"/>