# HG changeset patch
# User recetox
# Date 1709895331 0
# Node ID b566b27247f75d07c6fb740a86eb4caa4698ca65
# Parent  bc099c44001625f7c520984febf892c633e6e50c
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 4018b84dd3c735d16f488094f001a19e634fe1a2

diff -r bc099c440016 -r b566b27247f7 msp_out.sh
--- a/msp_out.sh	Tue Feb 27 16:20:31 2024 +0000
+++ b/msp_out.sh	Fri Mar 08 10:55:31 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 bc099c440016 -r b566b27247f7 qcxms_prod_run.xml
--- a/qcxms_prod_run.xml	Tue Feb 27 16:20:31 2024 +0000
+++ b/qcxms_prod_run.xml	Fri Mar 08 10:55:31 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="qcxms_production_run" name="QCxMS production run" version="@TOOL_VERSION@+galaxy1" profile="21.05">
+<tool id="qcxms_production_run" name="QCxMS production run" version="@TOOL_VERSION@+galaxy2" profile="22.09">
     <description>Production run to obtain a QCxMS simulated mass spectrum</description>
     
     <macros>
@@ -10,10 +10,7 @@
 
     <command detect_errors="exit_code"><![CDATA[
         python3 '${create_folder_structure}' &&
-        find TMPQCXMS/*/ -type d | xargs -I {} -P \${GALAXY_SLOTS:-1} sh -c 'cd {} && /qcxms_bin/qcxms --prod >> $log' &&
-        /qcxms_bin/getres &&
-        /plotms_bin/PlotMS.v.6.2.0/plotms &&
-        sh ${__tool_directory__}/msp_out.sh
+        (cd TMPQCXMS/*/ && /qcxms_bin/qcxms --prod) >> $log
     ]]></command>
 
     <environment_variables>
@@ -25,54 +22,50 @@
 import os
 import shutil
 
-#set in_collection = str("', '").join([str($f) for $f in $in_files])
-#set start_collection = str("', '").join([str($f) for $f in $start_files])
-#set xyz_collection = str("', '").join([str($f) for $f in $xyz_files])
+names = '$xyz_file.name'
+folder_name = names.split("_")[0]
 
-#set names = str("', '").join([str($f.name) for $f in $xyz_files])
-names = '$names'
-folder_names = [x.split("_")[0] for x in names]
-
-in_collection = '$in_collection'
-start_collection = '$start_collection'
-xyz_collection = '$xyz_collection'
 
 # Create a new output folder to store the result
 output_path = 'TMPQCXMS'
 os.makedirs(output_path, exist_ok=True)
 
-for folder_name, in_file, start_file, xyz_file in zip(folder_names, in_collection, start_collection, xyz_collection):
-    new_folder_path = os.path.join(output_path, folder_name)
-    os.makedirs(new_folder_path, exist_ok=True)
+new_folder_path = os.path.join(output_path, folder_name)
+os.makedirs(new_folder_path, exist_ok=True)
 
-    shutil.copy2(os.path.join(os.path.dirname(in_collection[0]), in_file), os.path.join(new_folder_path, 'qcxms.in'))
-    shutil.copy2(os.path.join(os.path.dirname(start_collection[0]), start_file), os.path.join(new_folder_path, 'qcxms.start'))
-    shutil.copy2(os.path.join(os.path.dirname(xyz_collection[0]), xyz_file), os.path.join(new_folder_path, 'start.xyz'))
+shutil.copy2(os.path.join(os.path.dirname('$in_file'), '$in_file'), os.path.join(new_folder_path, 'qcxms.in'))
+shutil.copy2(os.path.join(os.path.dirname('$start_file'), '$start_file'), os.path.join(new_folder_path, 'qcxms.start'))
+shutil.copy2(os.path.join(os.path.dirname('$xyz_file'), '$xyz_file'), os.path.join(new_folder_path, 'start.xyz'))
 
         </configfile>
     </configfiles>
 
     <inputs>
-        <param type="data_collection" collection_type="list" name="in_files" label="in files [.in]" format="in,txt,text"/>
-        <param type="data_collection" collection_type="list" name="start_files" label="start files [.start]" format="start,txt,text"/>
-        <param type="data_collection" collection_type="list" name="xyz_files" label="xyz files [.xyz]" format="xyz,txt,text"/>
+        <param type="data" name="in_file" label="in files [.in]" format="txt,text"/>
+        <param type="data" name="start_file" label="start files [.start]" format="txt,text"/>
+        <param type="data" name="xyz_file" label="xyz files [.xyz]" format="xyz,txt,text"/>
         <param name="store_extended_output" type="boolean" value="false" label="Store additional outputs" help="Output the logfile."/>
     </inputs>
 
     <outputs>
-        <data name="msp_output" format="msp" from_work_dir="simulated_spectra.msp" label="simulated_spectra.msp generated by ${tool.name} on ${on_string}"/>
-        <data name="log" format="txt" label="logfile of ${tool.name} on ${on_string}">
+        <data name="log" format="txt" label="logfile_of_${tool.id}_on_${on_string}">
             <filter>store_extended_output</filter>
         </data>
+        <data name="res_files" format="txt" from_work_dir="TMPQCXMS/*/qcxms.res" label="res files generated by ${tool.name} on ${on_string}"/>
     </outputs>
 
     <tests>
-        <test expect_failure="true"/>
+        <test expect_num_outputs="1">
+            <param name="in_file" value="TMP.1_qcxms_in.txt" ftype="txt"/>
+            <param name="start_file" value="TMP.1_qcxms_start.txt" ftype="txt"/>
+            <param name="xyz_file" value="TMP.1_start_xyz.txt" ftype="txt"/>
+            <output name="res_files" file="res_out.txt" ftype="txt"/>
+        </test>
     </tests>
 
     <help><![CDATA[
         The QCxMS production run tool is used to simulate mass spectra for a given molecule using the QCxMS (Quantum Chemistry by Mass Spectrometry) method. 
-        This tool generates simulated mass spectra based on the equilibrium structure of a molecule and allows you to perform QCxMS production runs.
+        This tool allows you to perform QCxMS production runs and generates res files which are further used by QCxMS get results tool to produce the simulated mass spectra.
         For detail information visit the documentation at https://xtb-docs.readthedocs.io/en/latest/qcxms_doc/qcxms_run.html#excecuting-the-production-runs
         ]]>
     </help>
diff -r bc099c440016 -r b566b27247f7 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 10:55:31 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 bc099c440016 -r b566b27247f7 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 10:55:31 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 bc099c440016 -r b566b27247f7 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 10:55:31 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 bc099c440016 -r b566b27247f7 test-data/output.msp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.msp	Fri Mar 08 10:55:31 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 bc099c440016 -r b566b27247f7 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 10:55:31 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 bc099c440016 -r b566b27247f7 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 10:55:31 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 bc099c440016 -r b566b27247f7 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 10:55:31 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 bc099c440016 -r b566b27247f7 test-data/res_out.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/res_out.txt	Fri Mar 08 10:55:31 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