comparison recetox_msfinder.xml @ 5:e7eff0c9baa3 draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit c6bc00f50c232c1c7cbb2e6f838c14a0c1c20e05
author recetox
date Wed, 24 Jan 2024 13:26:32 +0000
parents ae66b58846cd
children
comparison
equal deleted inserted replaced
4:ae66b58846cd 5:e7eff0c9baa3
1 <tool id="recetox_msfinder" name="RECETOX MsFinder" version="@TOOL_VERSION@+galaxy3"> 1 <tool id="recetox_msfinder" name="RECETOX MsFinder" version="@TOOL_VERSION@+galaxy4">
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 detect_errors="exit_code">
11 <![CDATA[ 11 <![CDATA[
12 mkdir output; 12 mkdir output;
13 sh ${write_param}; 13 sh ${write_param};
14 mono /MsFinder/MsFinder/bin/Debug/MsfinderConsoleApp.exe annotate -i "$input_data" -m 'MSFINDER.INI' -o 'output/result.msp'; 14 mono /MsFinder/MsFinder/bin/Debug/MsfinderConsoleApp.exe annotate -i '$input_data' -m 'MSFINDER.INI' -o 'output/result.msp';
15 [ -f output/log_smiles.smi ] && sed -i '1s/^/smiles\n/' output/log_smiles.smi;
15 [ -s output/result.msp ] || rm output/result.msp; 16 [ -s output/result.msp ] || rm output/result.msp;
16
17 ]]> 17 ]]>
18 </command> 18 </command>
19 19
20 <configfiles> 20 <configfiles>
21 <configfile name="write_param"> 21 <configfile name="write_param">
34 "IsUseRtInchikeyLibrary=True" \ 34 "IsUseRtInchikeyLibrary=True" \
35 "IsUsePredictedCcsForStructureElucidation=False" \ 35 "IsUsePredictedCcsForStructureElucidation=False" \
36 "IsUseCcsForFilteringCandidates=True" \ 36 "IsUseCcsForFilteringCandidates=True" \
37 "CcsToleranceForStructureElucidation=10" \ 37 "CcsToleranceForStructureElucidation=10" \
38 "CanExcuteMS2AdductSearch=False" \ 38 "CanExcuteMS2AdductSearch=False" \
39 "IsUseXlogpPrediction=False" >MSFINDER.INI 39 "IsUseXlogpPrediction=False" \
40 "ElementProbabilityCheck=$ElementProbabilityCheck" \
41 "IsotopicAbundanceTolerance=$IsotopicAbundanceTolerance" \
42 "TreeDepth=$TreeDepth" \
43 "$element_ratio_check" \
44 "IsUseEiFragmentDB=$IsUseEiFragmentDB" >MSFINDER.INI
45
46 #set element_selected = "\n".join([str($element) for $element in str($element_selection_option).split(",")])
47 printf "%s\n" "$element_selected" >> MSFINDER.INI
40 </configfile> 48 </configfile>
41 </configfiles> 49 </configfiles>
42 50
43 <inputs> 51 <inputs>
44 <expand macro="input" /> 52 <expand macro="input" />
45 <expand macro="parameter" /> 53 <expand macro="parameter" />
46 <!-- <section name="element_selection" title="Element Selection" expanded="true" help="Generate formula candidates that just contain the elements selected by the users."> 54 <param name="element_selection_option" type="select" label="Element selection" multiple="true" optional="true"
47 <expand macro="element_check_parameter" /> 55 help="Generate formula candidates that just contain the elements selected by the users. Check 'IsTmsMeoxDerivative' if you want to annotate EI-MS spectra.">
48 </section> --> 56 <expand macro="element_select" />
57 </param>
49 </inputs> 58 </inputs>
50 59
51 <outputs> 60 <outputs>
52 <expand macro="output" /> 61 <expand macro="output" />
53 </outputs> 62 </outputs>
57 <param name="input_data" value="test.msp" ftype="msp" /> 66 <param name="input_data" value="test.msp" ftype="msp" />
58 <output_collection name="output" type="list"> 67 <output_collection name="output" type="list">
59 <element name="result" file="out.msp" lines_diff="16"/> 68 <element name="result" file="out.msp" lines_diff="16"/>
60 </output_collection> 69 </output_collection>
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. --> 70 <!-- 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. -->
71 </test>
72 <test>
73 <param name="input_data" value="test.msp" ftype="msp" />
74 <param name="element_ratio_check" value="ExtendedRange=TRUE"/>
75 <param name="TreeDepth" value="3"/>
76 <param name="element_selection_option" value="Ocheck=True,Ncheck=True,Pcheck=True,Scheck=True,Fcheck=True,ClCheck=True,BrCheck=True,Icheck=True,SiCheck=True"/>
77 <output_collection name="output" type="list">
78 <element name="result" file="test2_out.msp" lines_diff="24"/>
79 </output_collection>
62 </test> 80 </test>
63 <test> 81 <test>
64 <param name="input_data" value="test_log.msp" ftype="msp" /> 82 <param name="input_data" value="test_log.msp" ftype="msp" />
65 <output_collection name="output" type="list"> 83 <output_collection name="output" type="list">
66 <element name="log_smiles" file="log_smiles.smi" /> 84 <element name="log_smiles" file="log_smiles.smi" />