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comparison combineAnnotations.xml @ 0:d6350a637d4a draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
author tomnl
date Fri, 24 May 2019 09:18:01 -0400
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1 <tool id="mspurity_combineannotations" name="msPurity.combineAnnotations" version="0.2.0">
2 <description>
3 Combine, score and rank metabolite annotation results
4 </description>
5
6 <macros>
7 <import>macros.xml</import>
8 </macros>
9
10 <expand macro="requirements">
11 </expand>
12
13 <stdio>
14 <exit_code range="1:" />
15 </stdio>
16 <command interpreter="Rscript"><![CDATA[
17 combineAnnotations.R
18 --sm_resultPth="$sm_resultPth"
19 --metfrag_resultPth="$metfrag_resultPth"
20 --sirius_csi_resultPth="$sirius_csi_resultPth"
21 --probmetab_resultPth="$probmetab_resultPth"
22 --sm_weight=$sm_weight
23 --metfrag_weight=$metfrag_weight
24 --sirius_csi_weight=$sirius_csi_weight
25 --probmetab_weight=$probmetab_weight
26 #if $create_new_database:
27 --create_new_database
28 #end if
29
30 ]]></command>
31 <inputs>
32 <param name="sm_resultPth" type="data" label="Spectral matching result" format="sqlite"
33 help="The SQLite database generated from msPurity.spectralMatching"/>
34 <param name="metfrag_resultPth" type="data" label="Metfrag result" format="tsv,tabular"
35 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"
37 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"
39 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" />
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" />
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" />
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" />
44 <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.
46 When False, the input SQLite database will be updated the results. Use False
47 if you want to reduce storage space being used."/>
48 </inputs>
49 <outputs>
50 <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" />
52 </outputs>
53 <tests>
54 <test>
55 <param name="sm_resultPth" value="spectralMatching_db_with_spectral_matching.sqlite" />
56 <param name="metfrag_resultPth" value="combineAnnotations_input_metfrag.tsv" />
57 <param name="sirius_csi_resultPth" value="combineAnnotations_input_sirus_csifingerid.tsv" />
58 <param name="probmetab_resultPth" value="combineAnnotations_input_probmetab.tsv" />
59 <output name="combined_annotations_tsv" file="combineAnnotations_combined_annotations.tsv" ftype="tsv" >
60 <assert_contents>
61 <has_n_columns n="32" />
62 </assert_contents>
63 </output>
64 <output name="combined_annotations_sqlite" file="combineAnnotations_combined_annotations.sqlite" ftype="sqlite" compare="sim_size"/>
65 </test>
66 </tests>
67 <help><![CDATA[
68 =============================================================
69 Combine annotation results
70 =============================================================
71 -----------
72 Description
73 -----------
74
75 Tool to combine the annotation results from msPurity spectral matching, MetFrag, Sirius CSI:FingerID and probmetab
76 based on weighted scores for each technique aligning each annotation by inchikey and XCMS grouped feature.
77
78 See Bioconductor documentation for more details, functions:
79 msPurity::combineAnnotation()
80
81 -----------
82 Outputs
83 -----------
84 * combined_annotation_sqlite
85 * combined_annotation_tsv
86
87 ]]></help>
88
89 <expand macro="citations" />
90
91 </tool>