# HG changeset patch
# User estrain
# Date 1593536923 14400
# Node ID 97b85c74d1c5d128b0e90eb1a4849135b5b878c6
# Parent  24f6296d3a0f73f5be1eafafa698ff80e0bb0ac1
Uploaded

diff -r 24f6296d3a0f -r 97b85c74d1c5 amrfinder/amrfinder.xml
--- a/amrfinder/amrfinder.xml	Tue Jun 30 12:55:24 2020 -0400
+++ b/amrfinder/amrfinder.xml	Tue Jun 30 13:08:43 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="amrfinder_gt" name="amrfinder_gt" version="@VERSION@+galaxy1">
+<tool id="amrfinderGT" name="amrfinder-plusGT" version="@VERSION@+galaxy1">
     <description>
       identifies AMR genes using either protein annotations or nucleotide sequence.
     </description>
@@ -34,8 +34,8 @@
     #end if
     -o results.tsv
     $report_common
-    #if $point_mut_all
-        --point_mut_all point_mutate.tsv
+    #if $mutational_all
+        --mutational_all mutation_all.tsv
     #end if
     $gpipe
     ]]>    </command>
@@ -98,14 +98,14 @@
         <param name="min_cov" argument="--coverage_min" type="float" min="0" max="1" value="0.5" label="Minimum coverage of the reference protein" />
         <param name="plus" type="boolean" truevalue="--plus" falsevalue="" label="Add the plus genes to the report" />
         <param name="report_common" type="boolean" truevalue="--report_common" falsevalue="" label="Suppress proteins common to a taxonomy group" />
-        <param name="point_mut_all" type="boolean" truevalue="true" falsevalue="false" label="Report all target positions of reference point mutations" />
+        <param name="mutation_all" type="boolean" truevalue="true" falsevalue="false" label="Report all target positions of mutations" />
         <param name="gpipe" type="boolean" truevalue="--gpipe" falsevalue="" label="Protein identifiers in the protein FASTA file have format gnl-project-accession" />
     </inputs>
 
     <outputs>
         <data name="result" format="tabular" from_work_dir="results.tsv" label="${tool.name} on ${on_string}: Result"/>
-        <data name="point_mutate" format="tabular" from_work_dir="point_mutate.tsv" label="${tool.name} on ${on_string}: Point mutate all">
-            <filter>point_mut_all</filter>
+        <data name="mutation_all" format="tabular" from_work_dir="mutation_all.tsv" label="${tool.name} on ${on_string}: All Mutations">
+            <filter>mutation_all</filter>
         </data>
     </outputs>