Mercurial > repos > recetox > recetox_msfinder
comparison recetox_msfinder.xml @ 4:ae66b58846cd draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit ad60bf881a8fd00546909c76d65ea3c6b65a4fe9
| author | recetox |
|---|---|
| date | Fri, 01 Dec 2023 09:23:21 +0000 |
| parents | d1f44632f206 |
| children | e7eff0c9baa3 |
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| 3:d1f44632f206 | 4:ae66b58846cd |
|---|---|
| 1 <tool id="recetox_msfinder" name="RECETOX MsFinder" version="@TOOL_VERSION@+galaxy2"> | 1 <tool id="recetox_msfinder" name="RECETOX MsFinder" version="@TOOL_VERSION@+galaxy3"> |
| 2 <description>Annotation of fragment peaks in mass spectral libraries.</description> | 2 <description>Annotation of fragment peaks in mass spectral libraries.</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="refs"/> | 6 <expand macro="refs"/> |
| 7 <expand macro="creator" /> | 7 <expand macro="creator" /> |
| 8 | 8 |
| 9 <expand macro="requirements" /> | 9 <expand macro="requirements" /> |
| 10 <command> | 10 <command> |
| 11 <![CDATA[ | 11 <![CDATA[ |
| 12 sh ${write_param} && | 12 mkdir output; |
| 13 mono /MsFinder/MsFinder/bin/Debug/MsfinderConsoleApp.exe annotate -i "$input_data" -m 'MSFINDER.INI' -o "$annotated_data" | 13 sh ${write_param}; |
| 14 mono /MsFinder/MsFinder/bin/Debug/MsfinderConsoleApp.exe annotate -i "$input_data" -m 'MSFINDER.INI' -o 'output/result.msp'; | |
| 15 [ -s output/result.msp ] || rm output/result.msp; | |
| 16 | |
| 14 ]]> | 17 ]]> |
| 15 </command> | 18 </command> |
| 16 | 19 |
| 17 <configfiles> | 20 <configfiles> |
| 18 <configfile name="write_param"> | 21 <configfile name="write_param"> |
| 50 </outputs> | 53 </outputs> |
| 51 | 54 |
| 52 <tests> | 55 <tests> |
| 53 <test> | 56 <test> |
| 54 <param name="input_data" value="test.msp" ftype="msp" /> | 57 <param name="input_data" value="test.msp" ftype="msp" /> |
| 55 <output name="annotated_data" file="out.msp" lines_diff="16 " /> | 58 <output_collection name="output" type="list"> |
| 59 <element name="result" file="out.msp" lines_diff="16"/> | |
| 60 </output_collection> | |
| 56 <!-- 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. --> | 61 <!-- 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. --> |
| 57 | 62 </test> |
| 63 <test> | |
| 64 <param name="input_data" value="test_log.msp" ftype="msp" /> | |
| 65 <output_collection name="output" type="list"> | |
| 66 <element name="log_smiles" file="log_smiles.smi" /> | |
| 67 </output_collection> | |
| 58 </test> | 68 </test> |
| 59 </tests> | 69 </tests> |
| 60 | 70 |
| 61 <help> | 71 <help> |
| 62 <![CDATA[ | 72 <![CDATA[ |