Mercurial > repos > recetox > qcxms_neutral_run
changeset 1:0d9d72ef658f draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 4018b84dd3c735d16f488094f001a19e634fe1a2
| author | recetox |
|---|---|
| date | Fri, 08 Mar 2024 10:55:21 +0000 |
| parents | 1d3fd08e50ff |
| children | 6c118de4b735 |
| files | msp_out.sh qcxms_neutral_run.xml test-data/TMP.1_qcxms_in.txt test-data/TMP.1_qcxms_start.txt test-data/TMP.1_start_xyz.txt 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 | 10 files changed, 102 insertions(+), 8 deletions(-) [+] |
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--- a/msp_out.sh Thu Feb 22 08:41:17 2024 +0000 +++ b/msp_out.sh Fri Mar 08 10:55:21 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`
--- a/qcxms_neutral_run.xml Thu Feb 22 08:41:17 2024 +0000 +++ b/qcxms_neutral_run.xml Fri Mar 08 10:55:21 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="qcxms_neutral_run" name="QCxMS neutral run" version="@TOOL_VERSION@+galaxy0" profile="21.05"> +<tool id="qcxms_neutral_run" name="QCxMS neutral run" version="@TOOL_VERSION@+galaxy1" profile="22.09"> <description>required as first step to prepare for the production runs</description> <macros> @@ -56,10 +56,10 @@ </configfiles> <inputs> - <param type="data" name="mol" label="Molecule 3D structure [.xzy]" format="xyz,txt" /> + <param type="data" name="mol" label="Molecule 3D structure [.xzy]" format="xyz" /> <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> + <option value="xtb1">GFN1-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]."> @@ -84,20 +84,20 @@ <filter>store_extended_output</filter> </data> - <collection name="coords1" format="txt" type="list" label="coords in files generated by ${tool.name} on ${on_string}" > + <collection name="coords1" format="txt" type="list" label="input 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}" > + <collection name="coords2" format="txt" type="list" label="input 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}" > + <collection name="coords3" format="txt" type="list" label="input 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"/> + <param name="mol" value="mol.xyz" ftype="xyz"/> <section name="keywords"> <param name="ntraj" value="2"/> </section>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TMP.1_qcxms_in.txt Fri Mar 08 10:55:21 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 10:55:21 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 10:55:21 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/output.msp Fri Mar 08 10:55:21 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 10:55:21 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 10:55:21 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