Mercurial > repos > tomnl > mspurity_combineannotations

annotate combineAnnotations.xml @ 13:4b7d43c49061 draft default tip

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 cb903cd93f9378cfb5eeb68512a54178dcea7bbc
author tomnl
date Wed, 27 Nov 2019 12:40:43 +0000
parents 8d5728c85337
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
b1dd803d5164 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit b6b8da66a6eef180ca8e333f98fc4b7575bac7b3
tomnl
parents: 8
diff changeset
1 <tool id="mspurity_combineannotations" name="msPurity.combineAnnotations" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
13
4b7d43c49061 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 10
diff changeset
2 <description>Combine, score and rank metabolite annotation results</description>
0
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
3 <macros>
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
4 <import>macros.xml</import>
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
5 </macros>
13
4b7d43c49061 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 10
diff changeset
6 <expand macro="requirements"/>
4b7d43c49061 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 10
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
4b7d43c49061 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 10
diff changeset
8 Rscript '$__tool_directory__/combineAnnotations.R'
4b7d43c49061 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 10
diff changeset
9 --sm_resultPth='$sm_resultPth'
4b7d43c49061 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 10
diff changeset
10 --metfrag_resultPth='$metfrag_resultPth'
4b7d43c49061 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 10
diff changeset
11 --sirius_csi_resultPth='$sirius_csi_resultPth'
4b7d43c49061 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 10
diff changeset
12 --probmetab_resultPth='$probmetab_resultPth'
4b7d43c49061 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 10
diff changeset
13 --ms1_lookup_resultPth='$ms1_lookup_resultPth'
10
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
14
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
15 #if $ms1_lookup_checkAdducts:
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
16 --ms1_lookup_checkAdducts
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
17 #end if
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
18
13
4b7d43c49061 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 10
diff changeset
19 --ms1_lookup_keepAdducts='$ms1_lookup_keepAdducts'
10
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
20 --ms1_lookup_dbSource=$ms1_lookup_dbSource
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
21
0
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
22 --sm_weight=$sm_weight
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
23 --metfrag_weight=$metfrag_weight
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
24 --sirius_csi_weight=$sirius_csi_weight
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
25 --probmetab_weight=$probmetab_weight
10
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
26 --ms1_lookup_weight=$ms1_lookup_weight
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
27 --biosim_weight=$biosim_weight
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
28
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
29
0
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
30 #if $create_new_database:
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
31 --create_new_database
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
32 #end if
4
68c405751ef6 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 14eafbdb65f491713d1314d77c454defd137c392
tomnl
parents: 3
diff changeset
33
10
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
34 --compoundDbType=$compoundDbTypeCond.compoundDbType
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
35
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
36 #if $compoundDbTypeCond.compoundDbType== 'sqlite'
13
4b7d43c49061 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 10
diff changeset
37 --compoundDbPth='$compoundDbTypeCond.compoundDbPth'
10
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
38 #end if
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
39
0
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
40
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
41 ]]></command>
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
42 <inputs>
10
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
43
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
44
13
4b7d43c49061 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 10
diff changeset
45 <param argument="--sm_resultPth" type="data" label="Spectral matching result" format="sqlite"
0
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
46 help="The SQLite database generated from msPurity.spectralMatching"/>
13
4b7d43c49061 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 10
diff changeset
47 <param argument="--metfrag_resultPth" type="data" label="Metfrag result" format="tsv,tabular" optional="true"
10
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
48 help="The result of the MetFrag analysis (requires a column indicating the XCMS group ID)"/>
13
4b7d43c49061 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 10
diff changeset
49 <param argument="--sirius_csi_resultPth" type="data" label="Sirius CSI:FingerID result" format="tsv,tabular" optional="true"
10
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
50 help="The result of the CSI:FingerID analysis (requires a column indicating the XCMS group ID)"/>
13
4b7d43c49061 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 10
diff changeset
51 <param argument="--probmetab_resultPth" type="data" label="Probmetab result" format="tsv,tabular" optional="true"
10
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
52 help="The result of the Probmetab analysis (requires a column indicating the XCMS group ID)"/>
13
4b7d43c49061 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 10
diff changeset
53 <param argument="--ms1_lookup_resultPth" type="data" label="MS1 Lookup result" format="tsv,tabular" optional="true"
10
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
54 help="The result of the a generic MS1 lookup annotation software (e.g. BEAMS can be used)"/>
13
4b7d43c49061 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 10
diff changeset
55 <param argument="--ms1_lookup_keepAdducts" type="text" label="MS1 lookup adducts to keep" optional="true"
10
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
56 help="Provide a list of adducts that should be used from the MS1 lookup (e.g. [M+H]+, [M+Na]+"/>
13
4b7d43c49061 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 10
diff changeset
57 <param argument="--ms1_lookup_checkAdducts" type="boolean" label="MS1 lookup check adducts to CAMERA"
10
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
58 help="Check if adducts match to those found in CAMERA (requires the database to have been created with CAMERA object"/>
13
4b7d43c49061 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 10
diff changeset
59 <param argument="--ms1_lookup_dbSource" type="select" label="MS1 lookup database source" help="Which database was used for the MS1 lookup" >
10
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
60 <option value="hmdb" selected="true">hmdb</option>
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
61 <option value="pubchem">pubchem</option>
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
62 <option value="kegg">kegg</option>
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
63 </param>
13
4b7d43c49061 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 10
diff changeset
64 <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" />
4b7d43c49061 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 10
diff changeset
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" />
4b7d43c49061 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 10
diff changeset
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" />
4b7d43c49061 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 10
diff changeset
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" />
4b7d43c49061 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 10
diff changeset
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" />
4b7d43c49061 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 10
diff changeset
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" />
4b7d43c49061 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 10
diff changeset
70 <param argument="--create_new_database" type="boolean" checked="true" label="Create a new database for the results?"
0
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
71 help="A copy will be made of the input SQLite spectral matching database and the results will be added to this copy.
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
72 When False, the input SQLite database will be updated the results. Use False
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
73 if you want to reduce storage space being used."/>
10
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
74
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
75 <conditional name="compoundDbTypeCond">
13
4b7d43c49061 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 10
diff changeset
76 <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)." >
10
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
77 <option value="sqlite" selected="true">SQLite</option>
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
78 <option value="local_config" >Locally configured MySQL, Postgres or SQLite database</option>
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
79 </param>
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
80 <when value="sqlite">
13
4b7d43c49061 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
tomnl
parents: 10
diff changeset
81 <param argument="--compoundDbPth" type="data" label="SQLite compound database pth" format="sqlite" help=""/>
10
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
82 </when>
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
83 <when value="local_config">
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
84 </when>
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
85 </conditional>
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
86
0
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
87 </inputs>
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
88 <outputs>
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
89 <data name="combined_annotations_sqlite" from_work_dir="combined_annotations.sqlite" format="sqlite" label="${tool.name} on ${on_string}: sqlite" />
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
90 <data name="combined_annotations_tsv" from_work_dir="combined_annotations.tsv" format="tsv" label="${tool.name} on ${on_string}: tsv" />
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
91 </outputs>
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
92 <tests>
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
93 <test>
10
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
94 <param name="sm_resultPth" value="combinedAnnotation_input_spectralMatching.sqlite" />
0
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
95 <param name="metfrag_resultPth" value="combineAnnotations_input_metfrag.tsv" />
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
96 <param name="sirius_csi_resultPth" value="combineAnnotations_input_sirus_csifingerid.tsv" />
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
97 <param name="probmetab_resultPth" value="combineAnnotations_input_probmetab.tsv" />
10
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
98 <param name="beams_resultPth" value="combineAnnotations_input_beams.tsv" />
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
99 <param name="compoundDbTypeCond|compoundDbPth" value="metab_compound_subset.sqlite" />
8d5728c85337 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 9
diff changeset
100 <output name="combined_annotations_tsv" file="combineAnnotations_combined_annotations.tsv" ftype="tsv" />
0
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
101 <output name="combined_annotations_sqlite" file="combineAnnotations_combined_annotations.sqlite" ftype="sqlite" compare="sim_size"/>
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
102 </test>
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
103 </tests>
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
104 <help><![CDATA[
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
105 =============================================================
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
106 Combine annotation results
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
107 =============================================================
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
108 -----------
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
109 Description
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
110 -----------
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
111
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
112 Tool to combine the annotation results from msPurity spectral matching, MetFrag, Sirius CSI:FingerID and probmetab
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
113 based on weighted scores for each technique aligning each annotation by inchikey and XCMS grouped feature.
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
114
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
115 See Bioconductor documentation for more details, functions:
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
116 msPurity::combineAnnotation()
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
117
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
118 -----------
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
119 Outputs
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
120 -----------
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
121 * combined_annotation_sqlite
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
122 * combined_annotation_tsv
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
123
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
124 ]]></help>
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
125
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
126 <expand macro="citations" />
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
127
d6350a637d4a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
tomnl
parents:
diff changeset
128 </tool>