Mercurial > repos > tomnl > mspurity_combineannotations

comparison combineAnnotations.xml @ 3:b22aa0a9fc25 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e05cb49ba56d359fec34f132d1c9ace582e5b483-dirty
author tomnl
date Tue, 18 Jun 2019 10:08:40 -0400
parents 75507d2e856c
children 68c405751ef6
comparison
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2:e912634293f5 3:b22aa0a9fc25
1 <tool id="mspurity_combineannotations" name="msPurity.combineAnnotations" version="0.2.1"> 1 <tool id="mspurity_combineannotations" name="msPurity.combineAnnotations" version="0.2.2">
2 <description> 2 <description>
3 Combine, score and rank metabolite annotation results 3 Combine, score and rank metabolite annotation results
4 </description> 4 </description>
5 5
6 <macros> 6 <macros>
24 --sirius_csi_weight=$sirius_csi_weight 24 --sirius_csi_weight=$sirius_csi_weight
25 --probmetab_weight=$probmetab_weight 25 --probmetab_weight=$probmetab_weight
26 #if $create_new_database: 26 #if $create_new_database:
27 --create_new_database 27 --create_new_database
28 #end if 28 #end if
29 #if $eic
30 --eic
31 #end if
29 32
30 ]]></command> 33 ]]></command>
31 <inputs> 34 <inputs>
32 <param name="sm_resultPth" type="data" label="Spectral matching result" format="sqlite" 35 <param name="sm_resultPth" type="data" label="Spectral matching result" format="sqlite"
33 help="The SQLite database generated from msPurity.spectralMatching"/> 36 help="The SQLite database generated from msPurity.spectralMatching"/>
34 <param name="metfrag_resultPth" type="data" label="Metfrag result" format="tsv,tabular" 37 <param name="metfrag_resultPth" type="data" label="Metfrag result" format="tsv,tabular" optional="true"
35 help="The result of the MetFrag analysis (requires a column indicating the XCMS group ID and fragmentation spectra ID)"/> 38 help="The result of the MetFrag analysis (requires a column indicating the XCMS group ID and fragmentation spectra ID)"/>
36 <param name="sirius_csi_resultPth" type="data" label="Sirius CSI:FingerID result" format="tsv,tabular" 39 <param name="sirius_csi_resultPth" type="data" label="Sirius CSI:FingerID result" format="tsv,tabular" optional="true"
37 help="The result of the CSI:FingerID analysis (requires a column indicating the XCMS group ID and fragmentation spectra ID)"/> 40 help="The result of the CSI:FingerID analysis (requires a column indicating the XCMS group ID and fragmentation spectra ID)"/>
38 <param name="probmetab_resultPth" type="data" label="Probmetab result" format="tsv,tabular" 41 <param name="probmetab_resultPth" type="data" label="Probmetab result" format="tsv,tabular" optional="true"
39 help="The result of the Probmetab analysis (requires a column indicating the XCMS group ID and fragmentation spectra ID)"/> 42 help="The result of the Probmetab analysis (requires a column indicating the XCMS group ID and fragmentation spectra ID)"/>
40 <param name="sm_weight" type="float" min="0.0" max="1.0" value="0.4" label="Spectral matching weight" help="all weights need to sum to 1" /> 43 <param name="sm_weight" type="float" min="0.0" max="1.0" value="0.4" label="Spectral matching weight" help="all weights need to sum to 1" />
41 <param name="metfrag_weight" type="float" min="0.0" max="1.0" value="0.25" label="Metfrag weight" help="all weights need to sum to 1" /> 44 <param name="metfrag_weight" type="float" min="0.0" max="1.0" value="0.25" label="Metfrag weight" help="all weights need to sum to 1" />
42 <param name="sirius_csi_weight" type="float" min="0.0" max="1.0" value="0.25" label="Sirius CSI:FingerID weight" help="all weights need to sum to 1" /> 45 <param name="sirius_csi_weight" type="float" min="0.0" max="1.0" value="0.25" label="Sirius CSI:FingerID weight" help="all weights need to sum to 1" />
43 <param name="probmetab_weight" type="float" min="0.0" max="1.0" value="0.1" label="Probmetab weight" help="all weights need to sum to 1" /> 46 <param name="probmetab_weight" type="float" min="0.0" max="1.0" value="0.1" label="Probmetab weight" help="all weights need to sum to 1" />
44 <param name="create_new_database" type="boolean" checked="true" label="Create a new database for the results?" 47 <param name="create_new_database" type="boolean" checked="true" label="Create a new database for the results?"
45 help="A copy will be made of the input SQLite spectral matching database and the results will be added to this copy. 48 help="A copy will be made of the input SQLite spectral matching database and the results will be added to this copy.
46 When False, the input SQLite database will be updated the results. Use False 49 When False, the input SQLite database will be updated the results. Use False
47 if you want to reduce storage space being used."/> 50 if you want to reduce storage space being used."/>
51 <param name="eic" type="boolean" label="Include EIC data?"
52 help="The Extracted Ion Chromatogram can be calculated for each peak and stored in
53 the database. Note, this will take considerable time for large datasets and
54 the resulting SQLite database can be large"/>
48 </inputs> 55 </inputs>
49 <outputs> 56 <outputs>
50 <data name="combined_annotations_sqlite" from_work_dir="combined_annotations.sqlite" format="sqlite" label="${tool.name} on ${on_string}: sqlite" /> 57 <data name="combined_annotations_sqlite" from_work_dir="combined_annotations.sqlite" format="sqlite" label="${tool.name} on ${on_string}: sqlite" />
51 <data name="combined_annotations_tsv" from_work_dir="combined_annotations.tsv" format="tsv" label="${tool.name} on ${on_string}: tsv" /> 58 <data name="combined_annotations_tsv" from_work_dir="combined_annotations.tsv" format="tsv" label="${tool.name} on ${on_string}: tsv" />
52 </outputs> 59 </outputs>