Mercurial > repos > recetox > qcxms_getres
changeset 0:ef51824f6d04 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 4018b84dd3c735d16f488094f001a19e634fe1a2
| author | recetox |
|---|---|
| date | Fri, 08 Mar 2024 10:55:44 +0000 |
| parents | |
| children | af8839475b43 |
| files | macros.xml msp_out.sh qcxms_getres.xml test-data/TMP.1_qcxms_in.txt test-data/TMP.1_qcxms_start.txt test-data/TMP.1_start_xyz.txt test-data/mol.xyz test-data/output.msp test-data/res_files/TMP.1_qcxms.txt test-data/res_files/TMP.2_qcxms.txt test-data/res_files/TMP.3_qcxms.txt test-data/res_out.txt |
| diffstat | 12 files changed, 226 insertions(+), 0 deletions(-) [+] |
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--- /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>
--- /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
--- /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>
--- /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
--- /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
--- /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
--- /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
--- /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 +
--- /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
--- /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