# HG changeset patch
# User recetox
# Date 1713267082 0
# Node ID 6c118de4b735d0323014f0b5037cda27d24fa943
# Parent  0d9d72ef658f213aec5f698882901576dee94f76
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 934037d9bacdb22293792c3d7bca9d2d34b65af9

diff -r 0d9d72ef658f -r 6c118de4b735 qcxms_neutral_run.xml
--- a/qcxms_neutral_run.xml	Fri Mar 08 10:55:21 2024 +0000
+++ b/qcxms_neutral_run.xml	Tue Apr 16 11:31:22 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="qcxms_neutral_run" name="QCxMS neutral run" version="@TOOL_VERSION@+galaxy1" profile="22.09">
+<tool id="qcxms_neutral_run" name="QCxMS neutral run" version="@TOOL_VERSION@+galaxy2" profile="22.09">
     <description>required as first step to prepare for the production runs</description>
     
     <macros>
@@ -24,13 +24,13 @@
 
     <configfiles>
         <configfile filename="qcxms.in"><![CDATA[
-            ${QC_Level}
-            #if $keywords.ntraj
-            ntraj  ${keywords.ntraj}
-            #end if
-            tmax  ${keywords.tmax} 
-            tinit  ${keywords.tinit} 
-            ieeatm  ${keywords.ieeatm}]]>
+${QC_Level}
+#if $keywords.ntraj
+ntraj  ${keywords.ntraj}
+#end if
+tmax  ${keywords.tmax} 
+tinit  ${keywords.tinit} 
+ieeatm  ${keywords.ieeatm}]]>
         </configfile>
         <configfile filename="rename.py">
 import os
@@ -59,7 +59,7 @@
         <param type="data" name="mol" label="Molecule 3D structure [.xzy]" format="xyz" />
         <param name="QC_Level" type="select" display="radio" label="QC Method">
             <option value="xtb2" selected="true">GFN2-xTB</option>
-            <option value="xtb1">GFN1-xTB</option>
+            <option value="xtb">GFN1-xTB</option>
         </param>
         <section name="keywords" title="Advanced method parameters" expanded="false" 
             help="List of advanced keywords to specify the method - for more information see [1].">
@@ -121,6 +121,33 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- test 2-->
+        <test expect_num_outputs="6">
+            <param name="mol" value="mol.xyz" ftype="xyz"/>
+            <param name="QC_Level" value="xtb"/>
+            <section name="keywords">
+                <param name="ntraj" value="2"/>
+            </section>
+            <param name="store_extended_output" value="true"/>
+            <output_collection name="coords1" type="list" count="2"/>
+            <output_collection name="coords2" type="list" count="2"/>
+            <output_collection name="coords3" type="list" count="2"/>
+            <output name="qcxms_out">
+                <assert_contents>
+                    <has_size value="174613" delta="300"/>
+                </assert_contents>
+            </output>
+            <output name="trajectory">
+                <assert_contents>
+                    <has_size value="22150" delta="300"/>
+                </assert_contents>
+            </output>
+            <output name="log">
+                <assert_contents>
+                    <has_text text="initializing GFN1-xTB"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
 
     <help><![CDATA[