# HG changeset patch
# User recetox
# Date 1709895344 0
# Node ID ef51824f6d0458b86c8257b192469afa9d3db06b

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 4018b84dd3c735d16f488094f001a19e634fe1a2

diff -r 000000000000 -r ef51824f6d04 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Mar 08 10:55:44 2024 +0000
@@ -0,0 +1,26 @@
+<macros>
+    <token name="@TOOL_VERSION@">5.2.1</token>
+    <xml name="requirements">
+        <requirements>
+            <container type="docker">recetox/qcxms-docker:@TOOL_VERSION@</container>
+        </requirements>
+    </xml>
+    <xml name="edam">
+        <edam_topics>
+            <edam_topic>topic_3332</edam_topic>
+        </edam_topics>
+        <edam_operations>
+            <edam_operation>operation_0297</edam_operation>
+        </edam_operations>
+    </xml>
+
+    <xml name="creator">
+        <creator>
+            <yield/>
+            <organization
+                url="https://www.recetox.muni.cz/"
+                email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
+                name="RECETOX MUNI" />
+        </creator>
+    </xml>
+</macros>
diff -r 000000000000 -r ef51824f6d04 msp_out.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/msp_out.sh	Fri Mar 08 10:55:44 2024 +0000
@@ -0,0 +1,11 @@
+#!/bin/sh
+
+molname=`sed -n '1{p;q}'  molname.txt`
+kword=$(grep 'NPOINTS' result.jdx)
+num_peaks=$(echo "$kword" | sed 's/^[^=]*=//')
+echo `pwd`
+sed -n '/PEAK/,/END/{/PEAK/!{/END/!p}}' result.jdx > temp.dat
+awk '{print $1, $2}' temp.dat > tempa.dat
+sed "1s/^/NAME: $molname\nNum Peaks: $num_peaks\n/" tempa.dat >> simulated_spectra.msp
+sed -i '$a\ ' simulated_spectra.msp
+rm temp.dat tempa.dat
\ No newline at end of file
diff -r 000000000000 -r ef51824f6d04 qcxms_getres.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qcxms_getres.xml	Fri Mar 08 10:55:44 2024 +0000
@@ -0,0 +1,75 @@
+<tool id="qcxms_getres" name="QCxMS get results" version="@TOOL_VERSION@+galaxy0" profile="22.09">
+    <description>Get result of the Production run to obtain a QCxMS simulated mass spectrum</description>
+    
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam"/>
+    <expand macro="creator"/>
+    <expand macro="requirements"/>
+
+    <command detect_errors="exit_code"><![CDATA[
+        python3 '${get_res}' &&
+        /plotms_bin/PlotMS.v.6.2.0/plotms &&
+        sh ${__tool_directory__}/msp_out.sh
+    ]]></command>
+
+    <configfiles>
+        <configfile name="get_res">
+#set res_collection = str("', '").join([str($f) for $f in $res_files])
+
+with open('$mol', 'r') as file:
+    lines = file.readlines()
+    molname = lines[1]
+
+with open('molname.txt', 'w') as file:
+    file.write(molname)
+
+input_files = '$res_collection'
+output_file = 'tmpqcxms.res'
+
+with open(output_file, 'w') as output:
+    for file_path in input_files:
+        with open(file_path, 'r') as input_file:
+            output.write(input_file.read())
+
+        </configfile>
+    </configfiles>
+
+    <inputs>
+        <param type="data" name="mol" label="Molecule 3D structure [.xzy]" format="xyz" />
+        <param type="data_collection" collection_type="list" name="res_files" label="res files [.res]" format="txt,text"/>
+    </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}"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="mol" value="mol.xyz" ftype="xyz"/>
+            <param name="res_files">
+                <collection type="list">
+                  <element name="res_files_1" value="res_files/TMP.1_qcxms.txt" />
+                  <element name="res_files_2" value="res_files/TMP.2_qcxms.txt" />
+                  <element name="res_files_3" value="res_files/TMP.3_qcxms.txt" />
+                </collection>
+            </param>
+            <output name="msp_output" file="output.msp" ftype="msp"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+        The QCxMS getres tool is used to simulate mass spectra for a given molecule. 
+        This tool take res and molecules files and generates simulated mass spectra.
+        ]]>
+    </help>
+
+    <citations>
+        <citation type="doi">10.1002/anie.201300158</citation>
+        <citation type="doi">10.1039/C4OB01668H</citation>
+        <citation type="doi">10.1021/jp5096618</citation>
+        <citation type="doi">10.1255/ejms.1313</citation>
+        <citation type="doi">10.1021/acs.jpca.6b02907</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r ef51824f6d04 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 10:55:44 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 000000000000 -r ef51824f6d04 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 10:55:44 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 000000000000 -r ef51824f6d04 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 10:55:44 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 000000000000 -r ef51824f6d04 test-data/mol.xyz
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mol.xyz	Fri Mar 08 10:55:44 2024 +0000
@@ -0,0 +1,20 @@
+18
+Lindane
+CL     -2.3574740887    0.2795224786    1.4453580379
+C      -1.5060254335   -0.0564753152   -0.1808833480
+C      -0.7409992814    1.1908990145   -0.6060928106
+C      -0.6154388189   -1.2913844585   -0.1359211653
+CL     -0.4997346103    1.0723730326   -2.4801609516
+C       0.6426193118    1.3751488924    0.0051864041
+CL     -1.5938731432   -2.7512128353    0.4462303221
+C       0.6645445824   -1.0841370821    0.6675278544
+CL      0.4618762434    2.1580321789    1.6895099878
+C       1.4344482422    0.0744384378    0.0415960811
+CL      1.6999230385   -2.6236054897    0.5561774969
+CL      3.0750505924    0.3596521318    0.8505522013
+H      -2.3252866268   -0.2277424186   -0.8540474772
+H      -1.3395941257    2.0737268925   -0.4863004684
+H      -0.3587814867   -1.5482350588   -1.1510624886
+H       1.1898183823    2.1143426895   -0.5496439934
+H       0.4745289683   -0.9351251125    1.7152343988
+H       1.6943985224   -0.1802178770   -0.9732601047
diff -r 000000000000 -r ef51824f6d04 test-data/output.msp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.msp	Fri Mar 08 10:55:44 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 000000000000 -r ef51824f6d04 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 10:55:44 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 000000000000 -r ef51824f6d04 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 10:55:44 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 000000000000 -r ef51824f6d04 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 10:55:44 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 000000000000 -r ef51824f6d04 test-data/res_out.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/res_out.txt	Fri Mar 08 10:55:44 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