Previous changeset 3:d1f44632f206 (2023-10-21) Next changeset 5:e7eff0c9baa3 (2024-01-24) |
Commit message:
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit ad60bf881a8fd00546909c76d65ea3c6b65a4fe9 |
modified:
macros.xml recetox_msfinder.xml |
added:
test-data/log_smiles.smi test-data/test_log.msp |
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diff -r d1f44632f206 -r ae66b58846cd macros.xml --- a/macros.xml Sat Oct 21 12:31:00 2023 +0000 +++ b/macros.xml Fri Dec 01 09:23:21 2023 +0000 |
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@@ -2,7 +2,7 @@ <token name="@TOOL_VERSION@">v3.5.2</token> <xml name="requirements"> <requirements> - <container type="docker">recetox/recetox-msfinder:v3.5.2-rcx0</container> + <container type="docker">recetox/recetox-msfinder:v3.5.2-rcx1</container> </requirements> </xml> <xml name="creator"> @@ -54,7 +54,10 @@ <param name="SiCheck" type="boolean" checked="True" truevalue="True" falsevalue="False" label="SiCheck" /> </xml> --> <xml name="output"> - <data name="annotated_data" format="msp" /> + <collection type="list" format="txt" name="output" label="${tool.name} on ${on_string}"> + <discover_datasets pattern="(?P<designation>.+)\.smi" directory="output" ext="smi" /> + <discover_datasets pattern="(?P<designation>.+)\.msp" directory="output" ext="msp" /> + </collection> </xml> <token name="@HELP@"><![CDATA[ |
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diff -r d1f44632f206 -r ae66b58846cd recetox_msfinder.xml --- a/recetox_msfinder.xml Sat Oct 21 12:31:00 2023 +0000 +++ b/recetox_msfinder.xml Fri Dec 01 09:23:21 2023 +0000 |
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@@ -1,4 +1,4 @@ -<tool id="recetox_msfinder" name="RECETOX MsFinder" version="@TOOL_VERSION@+galaxy2"> +<tool id="recetox_msfinder" name="RECETOX MsFinder" version="@TOOL_VERSION@+galaxy3"> <description>Annotation of fragment peaks in mass spectral libraries.</description> <macros> <import>macros.xml</import> @@ -9,8 +9,11 @@ <expand macro="requirements" /> <command> <![CDATA[ - sh ${write_param} && - mono /MsFinder/MsFinder/bin/Debug/MsfinderConsoleApp.exe annotate -i "$input_data" -m 'MSFINDER.INI' -o "$annotated_data" + mkdir output; + sh ${write_param}; + mono /MsFinder/MsFinder/bin/Debug/MsfinderConsoleApp.exe annotate -i "$input_data" -m 'MSFINDER.INI' -o 'output/result.msp'; + [ -s output/result.msp ] || rm output/result.msp; + ]]> </command> @@ -52,9 +55,16 @@ <tests> <test> <param name="input_data" value="test.msp" ftype="msp" /> - <output name="annotated_data" file="out.msp" lines_diff="16 " /> + <output_collection name="output" type="list"> + <element name="result" file="out.msp" lines_diff="16"/> + </output_collection> <!-- This is set to 16 since msfinder sometimes places double bonds between certain atoms and sometimes not - there are 16 such cases in this file. --> - + </test> + <test> + <param name="input_data" value="test_log.msp" ftype="msp" /> + <output_collection name="output" type="list"> + <element name="log_smiles" file="log_smiles.smi" /> + </output_collection> </test> </tests> |
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diff -r d1f44632f206 -r ae66b58846cd test-data/log_smiles.smi --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/log_smiles.smi Fri Dec 01 09:23:21 2023 +0000 |
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@@ -0,0 +1,1 @@ +Cl[Si]1Oc2ccccc2O1.[C-]#[O+].[C-]#[O+].[CH]1C=CC=C1.[Fe] |
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diff -r d1f44632f206 -r ae66b58846cd test-data/test_log.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_log.msp Fri Dec 01 09:23:21 2023 +0000 |
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@@ -0,0 +1,37 @@ +FORMULA: C13H9ClFeO4Si +COMMENT: SpectrumID: 1519953; Source: C4-1998-38-3; Class: Benzenoids; CASRN not real! +NAME: ((.eta.5-Cyclopentadienylironbiscarbonyl)(1,2-phenylenedioxysilyl)chloride complex +INCHI: InChI=1S/C6H4ClO2Si.C5H5.2CO.Fe/c7-10-8-5-3-1-2-4-6(5)9-10;1-2-4-5-3-1;2*1-2;/h1-4H;1-5H;;; +SMILES: Cl[Si]1Oc2ccccc2O1.[C-]#[O+].[C-]#[O+].[CH]1C=CC=C1.[Fe] +NUM PEAKS: 3 +292.0 999.0 +314.0 118.89 +348.0 734.24 + +FORMULA: C13H14O +COMMENT: SpectrumID: 1752764; Source: A1-13-956/SMS7-13; DOI: 10.1021/ol1029996; QI: 383; Class: Benzene and substituted derivatives; CASRN not real! |RI:1588| +NAME: ((1R*,2R*)-1-Methyl-2-phenylethynylcyclopropyl)methanol +RETENTIONINDEX: 1588.0 +INCHI: InChI=1S/C13H14O/c1-13(10-14)9-12(13)8-7-11-5-3-2-4-6-11/h2-6,12,14H,9-10H2,1H3/t12-,13-/m0/s1 +SMILES: C[C@@]1(CO)C[C@@H]1C#Cc1ccccc1 +NUM PEAKS: 20 +51.0 89.92 +63.0 89.92 +77.0 179.84 +88.0 39.96 +89.0 59.95 +91.0 49.95 +102.0 149.86 +113.0 49.95 +115.0 229.79 +127.0 139.87 +128.0 999.0 +129.0 199.82 +144.0 99.91 +155.0 119.89 +156.0 14.89 +157.0 1.1 +158.0 0.1 +186.0 39.96 +187.0 5.89 +188.0 0.5 \ No newline at end of file |