Mercurial > repos > recetox > qcxms_production_run

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Feb 22 08:41:32 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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/msp_out.sh	Thu Feb 22 08:41:32 2024 +0000
@@ -0,0 +1,11 @@
+#!/bin/sh
+
+molname=`sed -n '2{p;q}'  TMPQCXMS/TMP.1/start.xyz`
+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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qcxms_prod_run.xml	Thu Feb 22 08:41:32 2024 +0000
@@ -0,0 +1,87 @@
+<tool id="qcxms_production_run" name="QCxMS production run" version="@TOOL_VERSION@+galaxy0" profile="21.05">
+    <description>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 '${create_folder_structure}' &&
+        find TMPQCXMS/*/ -type d | xargs -I {} -P ${GALAXY_SLOTS} sh -c 'cd {} && /qcxms_bin/qcxms --prod >> $log' &&
+        /qcxms_bin/getres &&
+        /plotms_bin/PlotMS.v.6.2.0/plotms &&
+        sh ${__tool_directory__}/msp_out.sh
+    ]]></command>
+
+    <environment_variables>
+        <environment_variable name="OMP_NUM_THREADS">1,2,1</environment_variable>
+    </environment_variables>
+
+    <configfiles>
+        <configfile name="create_folder_structure">
+import os
+import shutil
+
+#set in_collection = str("', '").join([str($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 $xyz_files])
+
+#set names = str("', '").join([str($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)
+
+    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'))
+
+        </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 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}">
+            <filter>store_extended_output</filter>
+        </data>
+    </outputs>
+
+    <tests>
+        <test expect_failure="true"/>
+    </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.
+        For detail information visit the documentation at https://xtb-docs.readthedocs.io/en/latest/qcxms_doc/qcxms_run.html#excecuting-the-production-runs
+        ]]>
+    </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>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mol.xyz	Thu Feb 22 08:41:32 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