Mercurial > repos > computational-metabolomics > mspurity_combineannotations

comparison combineAnnotations.xml @ 2:d4376a743f7b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 242de155f13acd6cb88946e89b5196ac55578aa8"
author computational-metabolomics
date Wed, 01 Apr 2020 11:21:11 -0400
parents 7f3183988100
children 94a2b6571758
comparison
equal deleted inserted replaced
1:cf62d2c0104e 2:d4376a743f7b
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 Rscript '$__tool_directory__/combineAnnotations.R' 8 Rscript '$__tool_directory__/combineAnnotations.R'
9 --sm_resultPth='$sm_resultPth' 9 --sm_resultPth='$sm_resultPth'
10 --metfrag_resultPth='$metfrag_resultPth' 10 --metfrag_resultPth='$metfrag_resultPth'
11 --sirius_csi_resultPth='$sirius_csi_resultPth' 11 --sirius_csi_resultPth='$sirius_csi_resultPth'
12 --probmetab_resultPth='$probmetab_resultPth' 12
13 #if $probmetabCond.probmetabChoice == 'probmetab'
14 --probmetab_resultPth='$probmetabCond.probmetab_resultPth'
15 #end if
16
13 --ms1_lookup_resultPth='$ms1_lookup_resultPth' 17 --ms1_lookup_resultPth='$ms1_lookup_resultPth'
14 18
15 #if $ms1_lookup_checkAdducts: 19 #if $ms1_lookup_checkAdducts:
16 --ms1_lookup_checkAdducts 20 --ms1_lookup_checkAdducts
17 #end if 21 #end if
23 --metfrag_weight=$metfrag_weight 27 --metfrag_weight=$metfrag_weight
24 --sirius_csi_weight=$sirius_csi_weight 28 --sirius_csi_weight=$sirius_csi_weight
25 --probmetab_weight=$probmetab_weight 29 --probmetab_weight=$probmetab_weight
26 --ms1_lookup_weight=$ms1_lookup_weight 30 --ms1_lookup_weight=$ms1_lookup_weight
27 --biosim_weight=$biosim_weight 31 --biosim_weight=$biosim_weight
28 32
29 33
30 #if $create_new_database: 34 #if $create_new_database:
31 --create_new_database 35 --create_new_database
32 #end if 36 #end if
33 37
34 --compoundDbType=$compoundDbTypeCond.compoundDbType 38 --compoundDbType=$compoundDbTypeCond.compoundDbType
35 39
36 #if $compoundDbTypeCond.compoundDbType== 'sqlite' 40 #if $compoundDbTypeCond.compoundDbType== 'sqlite'
37 --compoundDbPth='$compoundDbTypeCond.compoundDbPth' 41 --compoundDbPth='$compoundDbTypeCond.compoundDbPth'
42 #end if
43
44 #if $summaryOutput:
45 --summaryOutput
38 #end if 46 #end if
39 47
40 48
41 ]]></command> 49 ]]></command>
42 <inputs> 50 <inputs>
46 help="The SQLite database generated from msPurity.spectralMatching"/> 54 help="The SQLite database generated from msPurity.spectralMatching"/>
47 <param argument="--metfrag_resultPth" type="data" label="Metfrag result" format="tsv,tabular" optional="true" 55 <param argument="--metfrag_resultPth" type="data" label="Metfrag result" format="tsv,tabular" optional="true"
48 help="The result of the MetFrag analysis (requires a column indicating the XCMS group ID)"/> 56 help="The result of the MetFrag analysis (requires a column indicating the XCMS group ID)"/>
49 <param argument="--sirius_csi_resultPth" type="data" label="Sirius CSI:FingerID result" format="tsv,tabular" optional="true" 57 <param argument="--sirius_csi_resultPth" type="data" label="Sirius CSI:FingerID result" format="tsv,tabular" optional="true"
50 help="The result of the CSI:FingerID analysis (requires a column indicating the XCMS group ID)"/> 58 help="The result of the CSI:FingerID analysis (requires a column indicating the XCMS group ID)"/>
51 <param argument="--probmetab_resultPth" type="data" label="Probmetab result" format="tsv,tabular" optional="true" 59 <conditional name="probmetabCond">
52 help="The result of the Probmetab analysis (requires a column indicating the XCMS group ID)"/> 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>
53 <param argument="--ms1_lookup_resultPth" type="data" label="MS1 Lookup result" format="tsv,tabular" optional="true" 72 <param argument="--ms1_lookup_resultPth" type="data" label="MS1 Lookup result" format="tsv,tabular" optional="true"
54 help="The result of the a generic MS1 lookup annotation software (e.g. BEAMS can be used)"/> 73 help="The result of the a generic MS1 lookup annotation software (e.g. BEAMS can be used)"/>
55 <param argument="--ms1_lookup_keepAdducts" type="text" label="MS1 lookup adducts to keep" optional="true" 74 <param argument="--ms1_lookup_keepAdducts" type="text" label="MS1 lookup adducts to keep" optional="true"
56 help="Provide a list of adducts that should be used from the MS1 lookup (e.g. [M+H]+, [M+Na]+"/> 75 help="Provide a list of adducts that should be used from the MS1 lookup (e.g. [M+H]+, [M+Na]+"/>
57 <param argument="--ms1_lookup_checkAdducts" type="boolean" label="MS1 lookup check adducts to CAMERA" 76 <param argument="--ms1_lookup_checkAdducts" type="boolean" label="MS1 lookup check adducts to CAMERA"
65 <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" /> 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" />
66 <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" /> 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" />
67 <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" /> 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" />
68 <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" /> 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" />
69 <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" /> 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"/>
70 <param argument="--create_new_database" type="boolean" checked="true" label="Create a new database for the results?" 90 <param argument="--create_new_database" type="boolean" checked="true" label="Create a new database for the results?"
71 help="A copy will be made of the input SQLite spectral matching database and the results will be added to this copy. 91 help="A copy will be made of the input SQLite spectral matching database and the results will be added to this copy.
72 When False, the input SQLite database will be updated the results. Use False 92 When False, the input SQLite database will be updated the results. Use False
73 if you want to reduce storage space being used."/> 93 if you want to reduce storage space being used."/>
74 94
91 </outputs> 111 </outputs>
92 <tests> 112 <tests>
93 <test> 113 <test>
94 <param name="sm_resultPth" value="combinedAnnotation_input_spectralMatching.sqlite" /> 114 <param name="sm_resultPth" value="combinedAnnotation_input_spectralMatching.sqlite" />
95 <param name="metfrag_resultPth" value="combineAnnotations_input_metfrag.tsv" /> 115 <param name="metfrag_resultPth" value="combineAnnotations_input_metfrag.tsv" />
96 <param name="sirius_csi_resultPth" value="combineAnnotations_input_sirus_csifingerid.tsv" /> 116 <param name="sirius_csi_resultPth" value="combineAnnotations_input_sirus_csifingerid.tsv" />
97 <param name="probmetab_resultPth" value="combineAnnotations_input_probmetab.tsv" /> 117 <param name="compoundDbTypeCond|compoundDbPth" value="metab_compound_subset.sqlite" />
98 <param name="beams_resultPth" value="combineAnnotations_input_beams.tsv" /> 118 <param name="beams_resultPth" value="combineAnnotations_input_beams.tsv" />
99 <param name="compoundDbTypeCond|compoundDbPth" value="metab_compound_subset.sqlite" /> 119 <param name="compoundDbTypeCond|compoundDbPth" value="metab_compound_subset.sqlite" />
100 <output name="combined_annotations_tsv" file="combineAnnotations_combined_annotations.tsv" ftype="tsv" /> 120 <output name="combined_annotations_tsv" file="combineAnnotations_combined_annotations.tsv" ftype="tsv" />
101 <output name="combined_annotations_sqlite" file="combineAnnotations_combined_annotations.sqlite" ftype="sqlite" compare="sim_size"/> 121 <output name="combined_annotations_sqlite" file="combineAnnotations_combined_annotations.sqlite" ftype="sqlite" compare="sim_size"/>
102 </test> 122 </test>