comparison recetox_msfinder.xml @ 0:7cda9aef13f3 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_msfinder commit f655a81cc6289f228ee7f58dc6b3e2d9eb2dc923
author recetox
date Tue, 13 Dec 2022 13:26:29 +0000
parents
children 29fc1af350f5
comparison
equal deleted inserted replaced
-1:000000000000 0:7cda9aef13f3
1 <tool id="recetox_msfinder" name="RECETOX MsFinder" version="@TOOL_VERSION@+galaxy0">
2 <description>Annotation of fragment peaks in mass spectral libraries.</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="creator" />
7
8 <expand macro="requirements" />
9 <command>
10 <![CDATA[
11 sh ${write_param} &&
12 mono /MsFinder/MsFinder/bin/Debug/MsfinderConsoleApp.exe annotate -i "$input_data" -m 'MSFINDER.INI' -o "$annotated_data"
13 ]]>
14 </command>
15
16 <configfiles>
17 <configfile name="write_param">
18 printf "%s\n" "Ms2Tolerance=$Ms2Tolerance" \
19 "IsTmsMeoxDerivative=$IsTmsMeoxDerivative" \
20 "RelativeAbundanceCutOff=$RelativeAbundanceCutOff" \
21 "Ms1Tolerance=$Ms1Tolerance" \
22 "MassToleranceType=$MassToleranceType" \
23 "StructurePredictionTimeOut=$StructurePredictionTimeOut" \
24 "Ocheck=$element_selection.Ocheck" \
25 "Ncheck=$element_selection.Ncheck" \
26 "Pcheck=$element_selection.Pcheck" \
27 "Scheck=$element_selection.Scheck" \
28 "Fcheck=$element_selection.Fcheck" \
29 "ClCheck=$element_selection.ClCheck" \
30 "BrCheck=$element_selection.BrCheck" \
31 "Icheck=$element_selection.Icheck" \
32 "SiCheck=$element_selection.SiCheck" \
33 "LewisAndSeniorCheck=$LewisAndSeniorCheck" \
34 "IsUseRtForFilteringCandidates=False" \
35 "RtToleranceForStructureElucidation=2.5" \
36 "IsUsePredictedRtForStructureElucidation=False" \
37 "Coeff_RtPrediction=-1" \
38 "Intercept_RtPrediction=-1" \
39 "IsUseRtInchikeyLibrary=True" \
40 "IsUsePredictedCcsForStructureElucidation=False" \
41 "IsUseCcsForFilteringCandidates=True" \
42 "CcsToleranceForStructureElucidation=10" \
43 "CanExcuteMS2AdductSearch=False" \
44 "IsUseXlogpPrediction=False" >MSFINDER.INI
45 </configfile>
46 </configfiles>
47
48 <inputs>
49 <expand macro="input" />
50 <expand macro="parameter" />
51 <section name="element_selection" title="Element Selection" expanded="true" help="Generate formula candidates that just contain the elements selected by the users.">
52 <expand macro="element_check_parameter" />
53 </section>
54 </inputs>
55
56 <outputs>
57 <expand macro="output" />
58 </outputs>
59
60 <tests>
61 <test>
62 <param name="input_data" value="test.msp" ftype="msp" />
63 <output name="annotated_data" file="out.msp" lines_diff="16 " />
64 <!-- 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. -->
65
66 </test>
67 </tests>
68
69 <help>
70 <![CDATA[
71 @HELP@
72 ]]>
73 </help>
74
75 <citations>
76 <expand macro="citations" />
77 </citations>
78 </tool>