Mercurial > repos > recetox > qcxms_neutral_run
changeset 0:1d3fd08e50ff draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 45ad41f2368834ab06929496fb17fc9a85b8e3c5
| author | recetox |
|---|---|
| date | Thu, 22 Feb 2024 08:41:17 +0000 |
| parents | |
| children | 0d9d72ef658f |
| files | macros.xml msp_out.sh qcxms_neutral_run.xml test-data/mol.xyz |
| diffstat | 4 files changed, 197 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Feb 22 08:41:17 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 08:41:17 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_neutral_run.xml Thu Feb 22 08:41:17 2024 +0000 @@ -0,0 +1,140 @@ +<tool id="qcxms_neutral_run" name="QCxMS neutral run" version="@TOOL_VERSION@+galaxy0" profile="21.05"> + <description>required as first step to prepare for the production runs</description> + + <macros> + <import>macros.xml</import> + </macros> + + <expand macro="edam"/> + <expand macro="creator"/> + <expand macro="requirements"/> + + <command detect_errors="exit_code"><![CDATA[ + ln -s '$mol' molecule.xyz && + cat qcxms.in && + /qcxms_bin/qcxms -i molecule.xyz >> '$log' && + /qcxms_bin/qcxms -i molecule.xyz >> '$log' && + python3 rename.py + + ]]></command> + + <environment_variables> + <environment_variable name="OMP_NUM_THREADS">1,2,1</environment_variable> + </environment_variables> + + <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}]]> + </configfile> + <configfile filename="rename.py"> +import os + +def rename_files_with_folder_name(folder_path): + if not os.path.exists(folder_path): + print(f"The folder '{folder_path}' does not exist.") + return + + for root, _, files in os.walk(folder_path): + for filename in files: + folder_name = os.path.basename(root) + new_filename = f"{folder_name}_{filename}" + + old_path = os.path.join(root, filename) + new_path = os.path.join(root, new_filename) + + os.rename(old_path, new_path) + +path = os.getcwd() + "/TMPQCXMS" +rename_files_with_folder_name(path) + </configfile> + </configfiles> + + <inputs> + <param type="data" name="mol" label="Molecule 3D structure [.xzy]" format="xyz,txt" /> + <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> + </param> + <section name="keywords" title="Advanced method parameters" expanded="false" + help="List of advanced keywords to specify the method - for more information see [1]."> + <param name="tmax" type="float" value="20.0" label="Maximum MD time (sampling) [ps]" + help="MD time for the mean-free-path (mfp) simulation in the EI mode. In the CID mode, this sets the number of time steps for the simulation + after fragmentation during internal energy scaling (implicit run type). For the explicit run type, the time for the collision MDs is fixed at 50 fs * number_of_atoms."/> + <param name="tinit" type="float" value="500.0" label="Initial Temperature [K]"/> + <param name="ieeatm" type="float" value="0.6" label="Impact excess energy (IEE) per atom [eV/atom]" /> + <param name="ntraj" type="integer" optional="true" min="2" label="Number of trajectories[#]" help="Default is 25 * no. of atoms if unspecified."/> + </section> + <param name="store_extended_output" type="boolean" value="false" label="Store additional outputs?" help="Output the logfile and generated trajectory."/> + </inputs> + + <outputs> + <data name="qcxms_out" format="txt" from_work_dir="qcxms.gs" label="qcxms.gs generated by ${tool.name} on ${on_string}"> + <filter>store_extended_output</filter> + </data> + <data name="trajectory" from_work_dir="trjM" format="txt" label="trajectories generated by ${tool.name} on ${on_string}"> + <filter>store_extended_output</filter> + </data> + <data name="log" format="txt" label="logfile of ${tool.name} on ${on_string}"> + <filter>store_extended_output</filter> + </data> + + <collection name="coords1" format="txt" type="list" label="coords in files generated by ${tool.name} on ${on_string}" > + <discover_datasets pattern="(?P<designation>.+)\.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}" > + <discover_datasets pattern="(?P<designation>.+)\.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}" > + <discover_datasets pattern="(?P<designation>.+)\.xyz" format="txt" directory="TMPQCXMS" recurse="true"/> + </collection> + </outputs> + + <tests> + <test expect_num_outputs="6"> + <param name="mol" value="mol.xyz" ftype="txt"/> + <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_size value="10518" delta="300"/> + </assert_contents> + </output> + </test> + </tests> + + <help><![CDATA[ + The QCxMS Neutral Run tool serves as the first step in preparing for production runs. The tool execute neutral runs for mass + spectrometry simulations using the GFN2-xTB and GFN-xTB quantum chemistry methods. 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 08:41:17 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