# HG changeset patch
# User recetox
# Date 1709895321 0
# Node ID 0d9d72ef658f213aec5f698882901576dee94f76
# Parent  1d3fd08e50ff19b745012f9b31bedbd1ad6fddf0
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 4018b84dd3c735d16f488094f001a19e634fe1a2

diff -r 1d3fd08e50ff -r 0d9d72ef658f msp_out.sh
--- a/msp_out.sh	Thu Feb 22 08:41:17 2024 +0000
+++ b/msp_out.sh	Fri Mar 08 10:55:21 2024 +0000
@@ -1,6 +1,6 @@
 #!/bin/sh
 
-molname=`sed -n '2{p;q}'  TMPQCXMS/TMP.1/start.xyz`
+molname=`sed -n '1{p;q}'  molname.txt`
 kword=$(grep 'NPOINTS' result.jdx)
 num_peaks=$(echo "$kword" | sed 's/^[^=]*=//')
 echo `pwd`
diff -r 1d3fd08e50ff -r 0d9d72ef658f qcxms_neutral_run.xml
--- a/qcxms_neutral_run.xml	Thu Feb 22 08:41:17 2024 +0000
+++ b/qcxms_neutral_run.xml	Fri Mar 08 10:55:21 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="qcxms_neutral_run" name="QCxMS neutral run" version="@TOOL_VERSION@+galaxy0" profile="21.05">
+<tool id="qcxms_neutral_run" name="QCxMS neutral run" version="@TOOL_VERSION@+galaxy1" profile="22.09">
     <description>required as first step to prepare for the production runs</description>
     
     <macros>
@@ -56,10 +56,10 @@
     </configfiles>
 
     <inputs>
-        <param type="data" name="mol" label="Molecule 3D structure [.xzy]" format="xyz,txt" />
+        <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="xtb">GFN-xTB</option>
+            <option value="xtb1">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].">
@@ -84,20 +84,20 @@
             <filter>store_extended_output</filter>
         </data>
 
-        <collection name="coords1" format="txt" type="list" label="coords in files generated by ${tool.name} on ${on_string}" >
+        <collection name="coords1" format="txt" type="list" label="input in files generated by ${tool.name} on ${on_string}" >
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.in" format="txt" directory="TMPQCXMS" recurse="true"/>
         </collection>
-        <collection name="coords2" format="txt" type="list" label="coords start files generated by ${tool.name} on ${on_string}" >
+        <collection name="coords2" format="txt" type="list" label="input start files generated by ${tool.name} on ${on_string}" >
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.start" format="txt" directory="TMPQCXMS" recurse="true"/>
         </collection>
-        <collection name="coords3" format="txt" type="list" label="coords xyz files generated by ${tool.name} on ${on_string}" >
+        <collection name="coords3" format="txt" type="list" label="input xyz files generated by ${tool.name} on ${on_string}" >
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.xyz" format="txt" directory="TMPQCXMS" recurse="true"/>
         </collection>
     </outputs>
 
     <tests>
         <test expect_num_outputs="6">
-            <param name="mol" value="mol.xyz" ftype="txt"/>
+            <param name="mol" value="mol.xyz" ftype="xyz"/>
             <section name="keywords">
                 <param name="ntraj" value="2"/>
             </section>
diff -r 1d3fd08e50ff -r 0d9d72ef658f test-data/TMP.1_qcxms_in.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TMP.1_qcxms_in.txt	Fri Mar 08 10:55:21 2024 +0000
@@ -0,0 +1,7 @@
+
+            xtb2
+            ntraj  2
+            tmax  20.0 
+            tinit  500.0 
+            ieeatm  0.6
+        
\ No newline at end of file
diff -r 1d3fd08e50ff -r 0d9d72ef658f test-data/TMP.1_qcxms_start.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TMP.1_qcxms_start.txt	Fri Mar 08 10:55:21 2024 +0000
@@ -0,0 +1,9 @@
+   1
+  0.23866896224151D+00
+  0.89173254224222D+04
+ -0.18091580000000D-03  0.53537546000000D-04  0.34508200000000D-04  0.50383142501519D+00
+  0.10322794000000D-03 -0.29410216000000D-03 -0.13830620000000D-03  0.50383142501512D+00
+ -0.12351298000000D-02  0.10941877000000D-02 -0.68662608000000D-03  0.10000000000000D+01
+  0.39194769000000D-04 -0.86113874000000D-03 -0.14824698000000D-03  0.99998640424089D+00
+  0.73344203000000D-03  0.11470574000000D-02 -0.89203254000000D-04  0.99998640424076D+00
+  0.13882303000000D-02 -0.37015395000000D-03  0.30430224000000D-03  0.99999999999989D+00
diff -r 1d3fd08e50ff -r 0d9d72ef658f test-data/TMP.1_start_xyz.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TMP.1_start_xyz.txt	Fri Mar 08 10:55:21 2024 +0000
@@ -0,0 +1,8 @@
+6
+6325
+C           -0.59857822001968       -0.02215985716365        0.13568410610374
+C            0.61205863904343       -0.05505705225983       -0.22393772541246
+H           -1.05122375889205        0.99067995917981        0.32453382107060
+H           -1.32624440512690       -0.87343794346470        0.13238115658175
+H            1.30113828028591        0.80217555351015       -0.27588079204055
+H            1.17175212384004       -1.04560876534258       -0.26477384393492
diff -r 1d3fd08e50ff -r 0d9d72ef658f test-data/output.msp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.msp	Fri Mar 08 10:55:21 2024 +0000
@@ -0,0 +1,52 @@
+NAME: Lindane
+Num Peaks: 49
+95.953354 29.195388847147174971
+96.956708 0.668804095247536257
+96.959630 0.006270038392945652
+97.950404 18.872816291174281389
+97.960062 0.002090012797648551
+98.953758 0.408597509163542982
+98.956680 0.006270038392945652
+99.947454 3.027383551460257394
+99.957112 0.001045006398824275
+100.950808 0.060610371892150218
+100.953730 0.001045006398824275
+112.007977 100.000000000000000000
+113.011331 6.469344248109893947
+113.014253 0.062015503068284489
+114.005027 31.968992563911168503
+114.014685 0.191684279973595856
+114.017607 0.002818886409876120
+115.008381 2.170542578675819456
+115.011303 0.016913318459256720
+116.011735 0.056377728197522396
+116.014657 0.002818886409876120
+117.015089 0.002818886409876120
+121.969004 48.616737474503565863
+122.972358 2.314913873279450307
+122.975280 0.028382084687048212
+123.966054 31.214972837163390551
+123.975712 0.030155965625322630
+123.978634 0.003547760585881026
+124.969408 1.333958011267293520
+124.972330 0.010643281757643079
+125.963104 4.931387222118633673
+125.972762 0.017738802929405131
+126.966458 0.184483555628484647
+126.969380 0.005321640878821540
+127.969812 0.001773880292940513
+147.984654 75.667375851606607284
+148.988008 4.978153862789445938
+148.990930 0.042283303452986920
+149.981704 48.524317372305198148
+149.991362 0.157857662942868432
+149.994284 0.002818886691764789
+150.985058 3.038759966527995626
+150.987980 0.036645528018447289
+151.978754 7.912614881227955976
+151.988412 0.087385490521223547
+151.991334 0.005637773383529577
+152.982108 0.467935188781944900
+152.985030 0.002818886691764789
+153.985462 0.019732207867858554
+ 
diff -r 1d3fd08e50ff -r 0d9d72ef658f test-data/res_files/TMP.1_qcxms.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/res_files/TMP.1_qcxms.txt	Fri Mar 08 10:55:21 2024 +0000
@@ -0,0 +1,5 @@
+ 0.0000000  1    1    1 1 1   17     1
+ 0.0000000  1    1    1 3 1   17     1
+ 0.0000000  1    1    2 2 1   17     1
+ 0.0000000  1    1    3 2 1   17     1
+ 1.0000000  1    1    4 1 3    1     6  6   6 17   2
diff -r 1d3fd08e50ff -r 0d9d72ef658f test-data/res_files/TMP.2_qcxms.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/res_files/TMP.2_qcxms.txt	Fri Mar 08 10:55:21 2024 +0000
@@ -0,0 +1,6 @@
+ 0.0000000  1    2    1 2 1   17     1
+ 0.0000000  1    2    1 3 1   17     1
+ 0.0000000  1    2    1 4 1   17     1
+ 0.0000001  1    2    2 1 2    1     1 17   1
+ 0.0000000  1    2    2 3 1   17     1
+ 0.9999999  1    2    3 1 3    1     5  6   6 17   1
diff -r 1d3fd08e50ff -r 0d9d72ef658f test-data/res_files/TMP.3_qcxms.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/res_files/TMP.3_qcxms.txt	Fri Mar 08 10:55:21 2024 +0000
@@ -0,0 +1,4 @@
+ 0.3707160  1    3    1 1 3    1     2  6   2 17   2
+ 0.0000000  1    3    1 3 1   17     1
+ 0.0000000  1    3    2 2 1   17     1
+ 0.6292840  1    3    3 1 3    1     4  6   4 17   2
diff -r 1d3fd08e50ff -r 0d9d72ef658f test-data/res_out.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/res_out.txt	Fri Mar 08 10:55:21 2024 +0000
@@ -0,0 +1,3 @@
+ 0.2874820  1    1    1 2 1    1     1
+ 0.2874820  1    1    1 3 1    1     1
+ 0.4250359  1    1    2 1 2    1     2  6   2