Mercurial > repos > computational-metabolomics > mspurity_combineannotations

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"
author computational-metabolomics
date Thu, 04 Mar 2021 12:21:39 +0000
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-1:000000000000 0:de93f6aac760
1 <tool id="mspurity_combineannotations" name="msPurity.combineAnnotations" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
2 <description>Combine, score and rank metabolite annotation results</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 Rscript '$__tool_directory__/combineAnnotations.R'
9 --sm_resultPth='$sm_resultPth'
10 --metfrag_resultPth='$metfrag_resultPth'
11 --sirius_csi_resultPth='$sirius_csi_resultPth'
12
13 #if $probmetabCond.probmetabChoice == 'probmetab'
14 --probmetab_resultPth='$probmetabCond.probmetab_resultPth'
15 #end if
16
17 --ms1_lookup_resultPth='$ms1_lookup_resultPth'
18
19 #if $ms1_lookup_checkAdducts:
20 --ms1_lookup_checkAdducts
21 #end if
22
23 --ms1_lookup_keepAdducts='$ms1_lookup_keepAdducts'
24 --ms1_lookup_dbSource=$ms1_lookup_dbSource
25
26 --sm_weight=$sm_weight
27 --metfrag_weight=$metfrag_weight
28 --sirius_csi_weight=$sirius_csi_weight
29 --probmetab_weight=$probmetab_weight
30 --ms1_lookup_weight=$ms1_lookup_weight
31 --biosim_weight=$biosim_weight
32
33
34 #if $create_new_database:
35 --create_new_database
36 #end if
37
38 --compoundDbType=$compoundDbTypeCond.compoundDbType
39
40 #if $compoundDbTypeCond.compoundDbType== 'sqlite'
41 --compoundDbPth='$compoundDbTypeCond.compoundDbPth'
42 #end if
43
44 #if $summaryOutput:
45 --summaryOutput
46 #end if
47
48
49 ]]></command>
50 <inputs>
51
52
53 <param argument="--sm_resultPth" type="data" label="Spectral matching result" format="sqlite"
54 help="The SQLite database generated from msPurity.spectralMatching"/>
55 <param argument="--metfrag_resultPth" type="data" label="Metfrag result" format="tsv,tabular" optional="true"
56 help="The result of the MetFrag analysis (requires a column indicating the XCMS group ID)"/>
57 <param argument="--sirius_csi_resultPth" type="data" label="Sirius CSI:FingerID result" format="tsv,tabular" optional="true"
58 help="The result of the CSI:FingerID analysis (requires a column indicating the XCMS group ID)"/>
59 <conditional name="probmetabCond">
60 <param name="probmetabChoice" type="select" label="Use probmetab data" help="The result of the Probmetab analysis" >
61 <option value="no_probmetab" selected="true" >Do not include probmetab results</option>
62 <option value="probmetab" >Include probmetab results</option>
63 </param>
64 <when value="probmetab">
65 <param argument="--probmetab_resultPth" type="data" label="Probmetab result" format="tsv,tabular" optional="true"
66 help="The result of the Probmetab analysis (requires a column indicating the XCMS group ID). Alternatively any ms1 annotation tool can be used
67 instead of probmetab"/>
68 </when>
69 <when value="no_probmetab">
70 </when>
71 </conditional>
72 <param argument="--ms1_lookup_resultPth" type="data" label="MS1 Lookup result" format="tsv,tabular" optional="true"
73 help="The result of the a generic MS1 lookup annotation software (e.g. BEAMS can be used)"/>
74 <param argument="--ms1_lookup_keepAdducts" type="text" label="MS1 lookup adducts to keep" optional="true"
75 help="Provide a list of adducts that should be used from the MS1 lookup (e.g. [M+H]+, [M+Na]+"/>
76 <param argument="--ms1_lookup_checkAdducts" type="boolean" label="MS1 lookup check adducts to CAMERA"
77 help="Check if adducts match to those found in CAMERA (requires the database to have been created with CAMERA object"/>
78 <param argument="--ms1_lookup_dbSource" type="select" label="MS1 lookup database source" help="Which database was used for the MS1 lookup" >
79 <option value="hmdb" selected="true">hmdb</option>
80 <option value="pubchem">pubchem</option>
81 <option value="kegg">kegg</option>
82 </param>
83 <param argument="--sm_weight" type="float" min="0.0" max="1.0" value="0.3" label="Spectral matching weight" help="all weights need to sum to 1" />
84 <param argument="--metfrag_weight" type="float" min="0.0" max="1.0" value="0.2" label="Metfrag weight" help="all weights need to sum to 1" />
85 <param argument="--sirius_csi_weight" type="float" min="0.0" max="1.0" value="0.2" label="Sirius CSI:FingerID weight" help="all weights need to sum to 1" />
86 <param argument="--probmetab_weight" type="float" min="0.0" max="1.0" value="0.0" label="Probmetab weight" help="all weights need to sum to 1" />
87 <param argument="--ms1_lookup_weight" type="float" min="0.0" max="1.0" value="0.05" label="MS1 Lookup weight" help="all weights need to sum to 1" />
88 <param argument="--biosim_weight" type="float" min="0.0" max="1.0" value="0.25" label="Biological similarity weight" help="all weights need to sum to 1" />
89 <param argument="--summaryOutput" type="boolean" checked="true" label="Create summary output" help="Create tab separated file of all annotations and features"/>
90 <param argument="--create_new_database" type="boolean" checked="true" label="Create a new database for the results?"
91 help="A copy will be made of the input SQLite spectral matching database and the results will be added to this copy.
92 When False, the input SQLite database will be updated the results. Use False
93 if you want to reduce storage space being used."/>
94
95 <conditional name="compoundDbTypeCond">
96 <param argument="--compoundDbType" type="select" label="compoundDbType" help="Database type for compound database to be used full database available on request - contact t.n.lawson@bham.ac.uk)." >
97 <option value="sqlite" selected="true">SQLite</option>
98 <option value="local_config" >Locally configured MySQL, Postgres or SQLite database</option>
99 </param>
100 <when value="sqlite">
101 <param argument="--compoundDbPth" type="data" label="SQLite compound database pth" format="sqlite" help=""/>
102 </when>
103 <when value="local_config">
104 </when>
105 </conditional>
106
107 </inputs>
108 <outputs>
109 <data name="combined_annotations_sqlite" from_work_dir="combined_annotations.sqlite" format="sqlite" label="${tool.name} on ${on_string}: sqlite" />
110 <data name="combined_annotations_tsv" from_work_dir="combined_annotations.tsv" format="tsv" label="${tool.name} on ${on_string}: tsv" />
111 </outputs>
112 <tests>
113 <test>
114 <param name="sm_resultPth" value="combinedAnnotation_input_spectralMatching.sqlite" />
115 <param name="metfrag_resultPth" value="combineAnnotations_input_metfrag.tsv" />
116 <param name="sirius_csi_resultPth" value="combineAnnotations_input_sirus_csifingerid.tsv" />
117 <param name="compoundDbTypeCond|compoundDbPth" value="metab_compound_subset.sqlite" />
118 <param name="beams_resultPth" value="combineAnnotations_input_beams.tsv" />
119 <param name="compoundDbTypeCond|compoundDbPth" value="metab_compound_subset.sqlite" />
120 <output name="combined_annotations_tsv" file="combineAnnotations_combined_annotations.tsv" ftype="tsv" />
121 <output name="combined_annotations_sqlite" file="combineAnnotations_combined_annotations.sqlite" ftype="sqlite" compare="sim_size"/>
122 </test>
123 </tests>
124 <help><![CDATA[
125 =============================================================
126 Combine annotation results
127 =============================================================
128 -----------
129 Description
130 -----------
131
132 Tool to combine the annotation results from msPurity spectral matching, MetFrag, Sirius CSI:FingerID and probmetab
133 based on weighted scores for each technique aligning each annotation by inchikey and XCMS grouped feature.
134
135 See Bioconductor documentation for more details, functions:
136 msPurity::combineAnnotation()
137
138 -----------
139 Outputs
140 -----------
141 * combined_annotation_sqlite
142 * combined_annotation_tsv
143
144 ]]></help>
145
146 <expand macro="citations" />
147
148 </tool>