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comparison combineAnnotations.xml @ 10:8d5728c85337 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
author tomnl
date Fri, 13 Sep 2019 12:01:27 -0400
parents b1dd803d5164
children 4b7d43c49061
comparison
equal deleted inserted replaced
9:b1dd803d5164 10:8d5728c85337
17 combineAnnotations.R 17 combineAnnotations.R
18 --sm_resultPth="$sm_resultPth" 18 --sm_resultPth="$sm_resultPth"
19 --metfrag_resultPth="$metfrag_resultPth" 19 --metfrag_resultPth="$metfrag_resultPth"
20 --sirius_csi_resultPth="$sirius_csi_resultPth" 20 --sirius_csi_resultPth="$sirius_csi_resultPth"
21 --probmetab_resultPth="$probmetab_resultPth" 21 --probmetab_resultPth="$probmetab_resultPth"
22
23 --ms1_lookup_resultPth=$ms1_lookup_resultPth
24
25 #if $ms1_lookup_checkAdducts:
26 --ms1_lookup_checkAdducts
27 #end if
28
29 --ms1_lookup_keepAdducts="$ms1_lookup_keepAdducts"
30 --ms1_lookup_dbSource=$ms1_lookup_dbSource
31
22 --sm_weight=$sm_weight 32 --sm_weight=$sm_weight
23 --metfrag_weight=$metfrag_weight 33 --metfrag_weight=$metfrag_weight
24 --sirius_csi_weight=$sirius_csi_weight 34 --sirius_csi_weight=$sirius_csi_weight
25 --probmetab_weight=$probmetab_weight 35 --probmetab_weight=$probmetab_weight
36 --ms1_lookup_weight=$ms1_lookup_weight
37 --biosim_weight=$biosim_weight
38
39
26 #if $create_new_database: 40 #if $create_new_database:
27 --create_new_database 41 --create_new_database
42 #end if
43
44 --compoundDbType=$compoundDbTypeCond.compoundDbType
45
46 #if $compoundDbTypeCond.compoundDbType== 'sqlite'
47 --compoundDbPth=$compoundDbTypeCond.compoundDbPth
28 #end if 48 #end if
29 49
30 50
31 ]]></command> 51 ]]></command>
32 <inputs> 52 <inputs>
33 <param name="sm_resultPth" type="data" label="Spectral matching result" format="sqlite" 53
54
55 <param name="sm_resultPth" type="data" label="Spectral matching result" format="sqlite"
34 help="The SQLite database generated from msPurity.spectralMatching"/> 56 help="The SQLite database generated from msPurity.spectralMatching"/>
35 <param name="metfrag_resultPth" type="data" label="Metfrag result" format="tsv,tabular" optional="true" 57 <param name="metfrag_resultPth" type="data" label="Metfrag result" format="tsv,tabular" optional="true"
36 help="The result of the MetFrag analysis (requires a column indicating the XCMS group ID and fragmentation spectra ID)"/> 58 help="The result of the MetFrag analysis (requires a column indicating the XCMS group ID)"/>
37 <param name="sirius_csi_resultPth" type="data" label="Sirius CSI:FingerID result" format="tsv,tabular" optional="true" 59 <param name="sirius_csi_resultPth" type="data" label="Sirius CSI:FingerID result" format="tsv,tabular" optional="true"
38 help="The result of the CSI:FingerID analysis (requires a column indicating the XCMS group ID and fragmentation spectra ID)"/> 60 help="The result of the CSI:FingerID analysis (requires a column indicating the XCMS group ID)"/>
39 <param name="probmetab_resultPth" type="data" label="Probmetab result" format="tsv,tabular" optional="true" 61 <param name="probmetab_resultPth" type="data" label="Probmetab result" format="tsv,tabular" optional="true"
40 help="The result of the Probmetab analysis (requires a column indicating the XCMS group ID and fragmentation spectra ID)"/> 62 help="The result of the Probmetab analysis (requires a column indicating the XCMS group ID)"/>
41 <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" /> 63 <param name="ms1_lookup_resultPth" type="data" label="MS1 Lookup result" format="tsv,tabular" optional="true"
42 <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" /> 64 help="The result of the a generic MS1 lookup annotation software (e.g. BEAMS can be used)"/>
43 <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" /> 65 <param name="ms1_lookup_keepAdducts" type="text" label="MS1 lookup adducts to keep" optional="true"
44 <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" /> 66 help="Provide a list of adducts that should be used from the MS1 lookup (e.g. [M+H]+, [M+Na]+"/>
45 <param name="create_new_database" type="boolean" checked="true" label="Create a new database for the results?" 67 <param name="ms1_lookup_checkAdducts" type="boolean" label="MS1 lookup check adducts to CAMERA"
68 help="Check if adducts match to those found in CAMERA (requires the database to have been created with CAMERA object"/>
69 <param name="ms1_lookup_dbSource" type="select" label="MS1 lookup database source" help="Which database was used for the MS1 lookup" >
70 <option value="hmdb" selected="true">hmdb</option>
71 <option value="pubchem">pubchem</option>
72 <option value="kegg">kegg</option>
73 </param>
74 <param name="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" />
75 <param name="metfrag_weight" type="float" min="0.0" max="1.0" value="0.2" label="Metfrag weight" help="all weights need to sum to 1" />
76 <param name="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" />
77 <param name="probmetab_weight" type="float" min="0.0" max="1.0" value="0.0" label="Probmetab weight" help="all weights need to sum to 1" />
78 <param name="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" />
79 <param name="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" />
80 <param name="create_new_database" type="boolean" checked="true" label="Create a new database for the results?"
46 help="A copy will be made of the input SQLite spectral matching database and the results will be added to this copy. 81 help="A copy will be made of the input SQLite spectral matching database and the results will be added to this copy.
47 When False, the input SQLite database will be updated the results. Use False 82 When False, the input SQLite database will be updated the results. Use False
48 if you want to reduce storage space being used."/> 83 if you want to reduce storage space being used."/>
84
85 <conditional name="compoundDbTypeCond">
86 <param name="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)." >
87 <option value="sqlite" selected="true">SQLite</option>
88 <option value="local_config" >Locally configured MySQL, Postgres or SQLite database</option>
89 </param>
90 <when value="sqlite">
91 <param type="data" name="compoundDbPth" label="SQLite compound database pth" format="sqlite" help=""/>
92 </when>
93 <when value="local_config">
94 </when>
95 <when value="msPurityData">
96 </when>
97 </conditional>
98
49 </inputs> 99 </inputs>
50 <outputs> 100 <outputs>
51 <data name="combined_annotations_sqlite" from_work_dir="combined_annotations.sqlite" format="sqlite" label="${tool.name} on ${on_string}: sqlite" /> 101 <data name="combined_annotations_sqlite" from_work_dir="combined_annotations.sqlite" format="sqlite" label="${tool.name} on ${on_string}: sqlite" />
52 <data name="combined_annotations_tsv" from_work_dir="combined_annotations.tsv" format="tsv" label="${tool.name} on ${on_string}: tsv" /> 102 <data name="combined_annotations_tsv" from_work_dir="combined_annotations.tsv" format="tsv" label="${tool.name} on ${on_string}: tsv" />
53 </outputs> 103 </outputs>
54 <tests> 104 <tests>
55 <test> 105 <test>
56 <param name="sm_resultPth" value="spectralMatching_db_with_spectral_matching.sqlite" /> 106 <param name="sm_resultPth" value="combinedAnnotation_input_spectralMatching.sqlite" />
57 <param name="metfrag_resultPth" value="combineAnnotations_input_metfrag.tsv" /> 107 <param name="metfrag_resultPth" value="combineAnnotations_input_metfrag.tsv" />
58 <param name="sirius_csi_resultPth" value="combineAnnotations_input_sirus_csifingerid.tsv" /> 108 <param name="sirius_csi_resultPth" value="combineAnnotations_input_sirus_csifingerid.tsv" />
59 <param name="probmetab_resultPth" value="combineAnnotations_input_probmetab.tsv" /> 109 <param name="probmetab_resultPth" value="combineAnnotations_input_probmetab.tsv" />
60 <output name="combined_annotations_tsv" file="combineAnnotations_combined_annotations.tsv" ftype="tsv" > 110 <param name="beams_resultPth" value="combineAnnotations_input_beams.tsv" />
61 <assert_contents> 111 <param name="compoundDbTypeCond|compoundDbPth" value="metab_compound_subset.sqlite" />
62 <has_n_columns n="32" /> 112 <output name="combined_annotations_tsv" file="combineAnnotations_combined_annotations.tsv" ftype="tsv" />
63 </assert_contents>
64 </output>
65 <output name="combined_annotations_sqlite" file="combineAnnotations_combined_annotations.sqlite" ftype="sqlite" compare="sim_size"/> 113 <output name="combined_annotations_sqlite" file="combineAnnotations_combined_annotations.sqlite" ftype="sqlite" compare="sim_size"/>
66 </test> 114 </test>
67 </tests> 115 </tests>
68 <help><![CDATA[ 116 <help><![CDATA[
69 ============================================================= 117 =============================================================