Mercurial > repos > recetox > ramclustr

annotate macros.xml @ 7:09cabbc3d12d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
author recetox
date Thu, 12 Oct 2023 13:30:54 +0000
parents 9b716db0a786
children d70dd1d6ac4d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
1 <macros>
4
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
2 <token name="@TOOL_VERSION@">1.3.0</token>
0
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
3
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
4 <xml name="creator">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
5 <creator>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
6 <person
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
7 givenName="Helge"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
8 familyName="Hecht"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
9 url="https://github.com/hechth"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
10 identifier="0000-0001-6744-996X" />
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
11 <person
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
12 givenName="Maksym"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
13 familyName="Skoryk"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
14 url="https://github.com/maximskorik"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
15 identifier="0000-0003-2056-8018" />
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
16 <person
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
17 givenName="Matej"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
18 familyName="Troják"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
19 url="https://github.com/xtrojak"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
20 identifier="0000-0003-0841-2707" />
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
21 <person
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
22 givenName="Martin"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
23 familyName="Čech"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
24 url="https://github.com/martenson"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
25 identifier="0000-0002-9318-1781" />
4
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
26 <person
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
27 givenName="Zargham"
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
28 familyName="Ahmad"
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
29 url="https://github.com/zargham-ahmad"
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
30 identifier="0000-0002-6096-224X" />
0
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
31 <organization
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
32 url="https://www.recetox.muni.cz/"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
33 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
34 name="RECETOX MUNI"/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
35 </creator>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
36 </xml>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
37
5
2410de08b55a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4a1bc7cba9745fd26e039b1629d4c9d9588ff5c0
recetox
parents: 4
diff changeset
38 <xml name="annotation">
2410de08b55a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4a1bc7cba9745fd26e039b1629d4c9d9588ff5c0
recetox
parents: 4
diff changeset
39 <edam_topics>
2410de08b55a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4a1bc7cba9745fd26e039b1629d4c9d9588ff5c0
recetox
parents: 4
diff changeset
40 <edam_topic>topic_3520</edam_topic>
2410de08b55a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4a1bc7cba9745fd26e039b1629d4c9d9588ff5c0
recetox
parents: 4
diff changeset
41 </edam_topics>
7
09cabbc3d12d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 6
diff changeset
42 </xml>
09cabbc3d12d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 6
diff changeset
43
09cabbc3d12d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 6
diff changeset
44 <xml name="refs">
5
2410de08b55a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4a1bc7cba9745fd26e039b1629d4c9d9588ff5c0
recetox
parents: 4
diff changeset
45 <xrefs>
2410de08b55a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4a1bc7cba9745fd26e039b1629d4c9d9588ff5c0
recetox
parents: 4
diff changeset
46 <xref type="bio.tools">ramclustr</xref>
2410de08b55a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4a1bc7cba9745fd26e039b1629d4c9d9588ff5c0
recetox
parents: 4
diff changeset
47 </xrefs>
7
09cabbc3d12d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 6
diff changeset
48 </xml>
5
2410de08b55a planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4a1bc7cba9745fd26e039b1629d4c9d9588ff5c0
recetox
parents: 4
diff changeset
49
0
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
50 <xml name="parameters_csv">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
51 <section name="ms_csv" title="Input MS Data as CSV" expanded="true">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
52 <param label="Input CSV" name="ms" type="data" format="csv"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
53 help="Features as columns, rows as samples. Column header in format mz_rt."/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
54 <param label="idMSMS" name="idmsms" type="data" format="csv" optional="true"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
55 help="Optional idMSMS / MSe csv data. Same dimension and names as in input CSV are required."/>
4
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
56 <param label="phenoData" name="csv_phenoData" type="data" format="csv" optional="true"
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
57 help="Optional csv containing phenoData."/>
0
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
58 </section>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
59 </xml>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
60
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
61 <xml name="parameters_xcms">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
62 <section name="xcms" title="Input MS Data as XCMS" expanded="true">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
63 <param name="input_xcms" label="Input XCMS" type="data" format="rdata.xcms.fillpeaks"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
64 help="Grouped feature data for clustering." />
4
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
65 </section>
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
66 </xml>
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
67
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
68 <xml name="parameters_recetox_aplcms">
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
69 <section name="ms_dataframe" title="Input MS Data as parquet (output from recetox-aplcms)" expanded="true">
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
70 <param label="Input MS1 featureDefinitions" name="ms1_featureDefinitions" type="data" format="parquet"
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
71 help="Metadata with columns: mz, rt, feature names containing MS data."/>
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
72 <param label="Input MS1 featureValues" name="ms1_featureValues" type="data" format="parquet"
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
73 help="data with rownames = sample names, colnames = feature names containing MS data."/>
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
74 <param label="phenoData" name="df_phenoData" type="data" format="tsv,csv" optional="true"
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
75 help="CSV/TSV file containing phenoData (optional)."/>
0
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
76 </section>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
77 </xml>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
78
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
79 <xml name="parameters_required">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
80 <param label="Sigma r" name="sr" type="float" value="0.5" help="Correlational similarity between features."/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
81 <param label="Correlation method" name="cor_method" type="select" display="radio"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
82 help="Choose correlational method to be used - see [1] for details.">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
83 <option value="pearson" selected="true">pearson</option>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
84 <option value="spearman">spearman</option>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
85 <option value="kendall">kendall</option>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
86 </param>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
87 <param label="Maximum RT difference" name="maxt" value="60" type="float"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
88 help="Maximum difference to calculate RT similarity - values beyond this are assigned zero similarity."/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
89 </xml>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
90
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
91 <xml name="main_parameters">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
92 <section name="clustering" title="Clustering" expanded="true">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
93 <param label="Clustering linkage method" name="linkage" type="select" display="radio"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
94 help="Choose hierarchical clustering linkage method - see [2] for details.">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
95 <option value="average" selected="true">average</option>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
96 <option value="ward.D">ward.D</option>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
97 <option value="ward.D2">ward.D2</option>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
98 <option value="single">single</option>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
99 <option value="complete">complete</option>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
100 <option value="mcquitty">mcquitty</option>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
101 <option value="median">median</option>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
102 <option value="centroid">centroid</option>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
103 </param>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
104 <param label="Minimal cluster size" name="minModuleSize" type="integer" value="2"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
105 help="Minimal size (number of features) of a cluster."/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
106 <param label="Maximal tree height" name="hmax" type="float" value="0.3"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
107 help="Cut the Hierarchical Cluster Analysis tree at this height, see [3] for details."/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
108 <param label="Use deepSplit" name="deepSplit" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
109 help="Check to produce more smaller clusters, uncheck for fewer bigger clusters, see [3] for details."/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
110 </section>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
111
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
112 <section name="normalisation" title="Normalisation" expanded="true">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
113 <conditional name="normalisation_method">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
114 <param label="Normalisation method" name="normalize" type="select" display="radio"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
115 help="Choose method for normalization of feature intensities.">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
116 <option value="none" selected="true">none</option>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
117 <option value="TIC">TIC</option>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
118 <option value="quantile">quantile</option>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
119 <option value="batch.qc">batch.qc</option>
4
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
120 <option value="qc">qc</option>
0
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
121 </param>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
122 <when value="batch.qc">
4
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
123 <param label="Metadata details" name="batch_order_qc" type="data" format="csv"
0
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
124 help="CSV with sample names (or indices, currently not handled) on rows and columns with:
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
125 batch number ('batch'), position in sequence ('order'), and whether it is a QC sample or not
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
126 ('qc' with true/false OR 'sampleType' with 'sample/qc/blank')."/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
127 <param label="QC injection range" name="qc_inj_range" type="integer" value="20"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
128 help="How many injections around each injection are to be scanned for presence of QC samples?
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
129 A good rule of thumb is between 1 and 3 times the typical
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
130 injection span between QC injections. i.e. if you inject QC ever 7 samples, set this to
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
131 between 7 and 21. Smaller values provide more local precision but make normalization sensitive
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
132 to individual poor outliers (though these are first removed using the boxplot function outlier
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
133 detection), while wider values provide less local precision in normalization but better
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
134 stability to individual peak areas."/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
135 </when>
4
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
136 <when value="qc">
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
137 <param label="Metadata details" name="batch_order_qc" type="data" format="csv" optional="true"
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
138 help="CSV with sample names (or indices, currently not handled) on rows and columns with:
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
139 batch number ('batch'), position in sequence ('order'), and whether it is a QC sample or not
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
140 ('qc' with true/false OR 'sampleType' with 'sample/qc/blank')."/>
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
141 <param label="p.cut" name="p_cut" type="float" value="0.05"
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
142 help="Numeric when run order correction is applied, only features showing a run order vs
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
143 signal with a linear p-value (after FDR correction) &lt; p.cut will be adjusted. also requires
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
144 r-squared &lt; rsq.cut."/>
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
145 <param label="rsq.cut" name="rsq_cut" type="float" value="0.1"
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
146 help="Numeric when run order correction is applied, only features showing a run order vs signal
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
147 with a linear r-squared &gt; rsq.cut will be adjusted. also requires p values &lt; p.cut."/>
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
148 <param label="p.adjust" name="p_adjust" type="text" value="none"
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
149 help="Which p-value adjustment should be used? one of ['holm', 'hochberg', 'hommel', 'bonferroni', 'BH',
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
150 'BY', 'fdr', 'none']"/>
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
151 </when>
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
152 <when value="none"/>
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
153 <when value="TIC"/>
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
154 <when value="quantile"/>
0
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
155 </conditional>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
156 </section>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
157
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
158 <section name="performance" title="Performance">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
159 <param label="Blocksize" name="blocksize" type="integer" value="2000"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
160 help="Number of features processed in one block."/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
161 <param label="Blocksize factor" name="mult" type="integer" value="5"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
162 help="Factor to scale blocksize to influence processing speed."/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
163 </section>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
164
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
165 <section name="msp_output_details" title="MSP output">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
166 <param label="Merge MSP Files" name="merge_msp" type="boolean" truevalue="TRUE" falsevalue="FALSE"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
167 checked="true" help="Merge all MSP in one file or export one MSP per spectra."/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
168 <param label="m/z decimal places" name="mzdec" type="integer" value="6"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
169 help="Number of decimal places used in printing m/z values."/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
170 <!--
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
171 Currently not forwarded because the MSP is exported always manually afterwards
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
172 <param label="mspout" name="mspout" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" help="write msp formatted spectra to file?" />
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
173 -->
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
174 </section>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
175
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
176 <section name="extras" title="Extras">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
177 <param label="RT only low n" name="rt_only_low_n" type="boolean" truevalue="TRUE" falsevalue="FALSE"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
178 checked="true"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
179 help="At low injection numbers, correlational relationships of peak intensities may be unreliable.
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
180 By default, RAMClustR will simply ignore the correlational Sigma r value and cluster on retention time alone.
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
181 If you wish to use correlation with at n less than 5, set this value to FALSE."/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
182 <param label="Replace zeros" name="replace_zeros" type="boolean" truevalue="TRUE" falsevalue="FALSE"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
183 checked="true"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
184 help="NA, NaN, and Inf values are replaced with zero, and zero values are sometimes returned from
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
185 peak peaking. When TRUE, zero values will be replaced with a small amount of noise, with noise level
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
186 set based on the detected signal intensities for that feature."/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
187 <param label="Experimental design metadata" name="ExpDes" type="data" format="csv" optional="true"
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
188 help="Definition of experimental design in CSV format." />
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
189 </section>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
190 </xml>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
191
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
192 <xml name="output_msp">
4
050cfef6ba65 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 1
diff changeset
193 <collection label="Mass spectra from ${tool.name} on ${on_string} list" name="mass_spectra_collection" type="list">
0
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
194 <discover_datasets pattern="__name_and_ext__" directory="spectra" recurse="true" ext="msp"/>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
195 <filter>not msp_output_details['merge_msp']</filter>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
196 </collection>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
197 <data label="Mass spectra from ${tool.name} on ${on_string}" name="mass_spectra_merged" format="msp">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
198 <filter>msp_output_details['merge_msp']</filter>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
199 </data>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
200 </xml>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
201
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
202 <xml name="citations">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
203 <citations>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
204 <!-- Example of annotating a citation using a BibTex entry. -->
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
205 <citation type="bibtex">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
206 @article{Broeckling2014e,
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
207 abstract = {Metabolomic data are frequently acquired using chromatographically coupled mass spectrometry
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
208 (MS) platforms. For such datasets, the first step in data analysis relies on feature detection, where a
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
209 feature is defined by a mass and retention time. While a feature typically is derived from a single
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
210 compound, a spectrum of mass signals is more a more-accurate representation of the mass spectrometric
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
211 signal for a given metabolite. Here, we report a novel feature grouping method that operates in an
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
212 unsupervised manner to group signals from MS data into spectra without relying on predictability of the
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
213 in-source phenomenon. We additionally address a fundamental bottleneck in metabolomics, annotation of MS
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
214 level signals, by incorporating indiscriminant MS/MS (idMS/MS) data implicitly: feature detection is
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
215 performed on both MS and idMS/MS data, and feature-feature relationships are determined simultaneously
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
216 from the MS and idMS/MS data. This approach facilitates identification of metabolites using in-source MS
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
217 and/or idMS/MS spectra from a single experiment, reduces quantitative analytical variation compared to
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
218 single-feature measures, and decreases false positive annotations of unpredictable phenomenon as novel
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
219 compounds. This tool is released as a freely available R package, called RAMClustR, and is sufficiently
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
220 versatile to group features from any chromatographic-spectrometric platform or feature-finding software.
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
221 {\textcopyright} 2014 American Chemical Society.},
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
222 author = {Broeckling, C. D. and Afsar, F. A. and Neumann, S. and Ben-Hur, A. and Prenni, J. E.},
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
223 doi = {10.1021/ac501530d},
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
224 issn = {15206882},
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
225 journal = {Analytical Chemistry},
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
226 number = {14},
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
227 pages = {6812--6817},
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
228 pmid = {24927477},
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
229 title = {{RAMClust: A novel feature clustering method enables spectral-matching-based annotation for
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
230 metabolomics data}},
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
231 volume = {86},
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
232 year = {2014}
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
233 }
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
234 </citation>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
235 </citations>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
236 </xml>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
237
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
238 <token name="@HELP@">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
239 <![CDATA[
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
240 Documentation
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
241 For documentation on the tool see https://github.com/cbroeckl/RAMClustR/blob/master/vignettes/RAMClustR.Rmd
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
242
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
243 Upstream Tools
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
244 +------------------------------+-------------------------------+----------------------+---------------------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
245 | Name | Output File | Format | Parameter |
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
246 +==============================+===============================+======================+=====================+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
247 | xcms | xset.fillPeaks.RData | rdata.xcms.fillpeaks | xcmsObj |
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
248 +------------------------------+-------------------------------+----------------------+---------------------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
249 | RAMClustR define experiment | Table with experiment details | csv | Experimental design |
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
250 +------------------------------+-------------------------------+----------------------+---------------------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
251
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
252 The tool takes an **xcmsSet** object as input and extracts all relevant information.
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
253
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
254 +-------+------------------------+--------+------------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
255 | Name | Output File | Format | Parameter |
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
256 +=======+========================+========+============+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
257 | ??? | Feature Table with MS1 | csv | ms |
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
258 +-------+------------------------+--------+------------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
259 | ??? | Feature Table with MS2 | csv | idmsms |
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
260 +-------+------------------------+--------+------------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
261
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
262 Alternatively, the tool takes a **csv** table as input which has to fulfill the following requirements
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
263
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
264 (1) no more than one sample (or file) name column and one feature name row;
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
265 (2) feature names that contain the mass and retention times, separated by a constant delimiter; and
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
266 (3) features in columns and samples in rows.
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
267
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
268 +----------------------+-------------------+-------------------+--------------------+--------------------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
269 | sample | 100.88_262.464 | 100.01_423.699 | 100.003_128.313 | 100.0057_154.686 |
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
270 +======================+===================+===================+====================+====================+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
271 | 10_qc_16x_dil_milliq | 0 | 195953.6376 | 0 | 0 |
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
272 +----------------------+-------------------+-------------------+--------------------+--------------------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
273 | 11_qc_8x_dil_milliq | 0 | 117742.1828 | 4247300.664 | 0 |
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
274 +----------------------+-------------------+-------------------+--------------------+--------------------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
275 | 12_qc_32x_dil_milliq | 4470859.38 | 0 | 2206092.112 | 0 |
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
276 +----------------------+-------------------+-------------------+--------------------+--------------------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
277 | 15_qc_16x_dil_milliq | 0 | 0 | 2767477.481 | 0 |
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
278 +----------------------+-------------------+-------------------+--------------------+--------------------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
279
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
280
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
281 Downstream Tools
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
282 The output is a msp file or a collection of msp files, with additional Spec Abundance file.
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
283
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
284 +---------+--------------+----------------------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
285 | Name | Output File | Format |
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
286 +=========+==============+======================+
6
9b716db0a786 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 5
diff changeset
287 | matchms | Mass Spectra | collection (tgz/msp) |
0
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
288 +---------+--------------+----------------------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
289
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
290 @GENERAL_HELP@
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
291 ]]>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
292 </token>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
293
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
294 <token name="@GENERAL_HELP@">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
295 Background
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
296 Metabolomics
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
297 Metabolomics is frequently performed using chromatographically coupled mass spectrometry, with gas
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
298 chromatography, liquid chromatography, and capillary electrophoresis being the most frequently utilized
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
299 methods of separation. The coupling of chromatography to mass spectrometry is enabled with an
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
300 appropriate ionization source - electron impact (EI) for gas phase separations and electrospray
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
301 ionization (ESI) for liquid phase separations. XCMS is a commonly used tool to detect all the signals
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
302 from a metabolomics dataset, generating aligned features, where a feature is represented by a mass and
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
303 retention time. Each feature is presumed to derive from a single compound. However, each compound is
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
304 represented by several features. With any ionization method, isotopic peaks will be observed reflective
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
305 of the elemental composition of the analyte. In EI, fragmentation is a byproduct of ionization, and has
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
306 driven the generation of large mass spectral libraries. In ESI, in-source fragmentation frequently
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
307 occurs, the magnitude of which is compound dependent, with more labile compounds being more prone to
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
308 in-source fragmentation. ESI can also product multiple adduct forms (protonated, potassiated, sodiated,
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
309 ammoniated...), and can produce multimers (i.e. [2M+H]+, [3M+K]+, etc) and multiple charged species
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
310 ([M+2H]++). This can become further complicated by considering combinations of these phenomena. For
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
311 example [2M+3H]+++ (triply charged dimer) or an in-source fragment of a dimer.
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
312
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
313 RAMClustR approach
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
314 RAMClustR was designed to group features designed from the same compound using an approach which is
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
315 **1.** unsupervised, **2.** platform agnostic, and **3.** devoid of curated rules, as the depth of
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
316 understanding of these processes is insufficient to enable accurate curation/prediction of all phenomenon
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
317 that may occur. We achieve this by making two assumptions. The first is that two features derived
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
318 from the same compound with have (approximately) the same retention time. The second is that two
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
319 features derived from the same compound will have (approximately) the same quantitative trend across
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
320 all samples in the xcms sample set. From these assumptions, we can calculate a retention time
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
321 similarity score and a correlational similarity score for each feature pair. A high similarity score
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
322 for both retention time and correlation indicates a strong probability that two features derive from
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
323 the same compound. Since both conditions must be met, the product of the two similarity scores provides
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
324 the best approximation of the total similarity score - i.e. a feature pair with retention time similarity
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
325 of 1 and correlational similarity of 0 is unlikely to derive from one compound - 1 x 0 = 0, the final
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
326 similarity score is zero, indicating the two features represent two different compounds. Similarly, a
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
327 feature pair with retention time similarity of 0 and correlational similarity of 1 is unlikely to derive
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
328 from one compound - 0 x 1 = 0. Alternatively - a feature pair with retention time similarity of 1 and
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
329 correlational similarity of 1 is likely to derive from one compound - 1 x 1 = 1.
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
330
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
331 The RAMClustR algorithm is built on creating similarity scores for all pairs of features, submitting
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
332 this score matrix for hierarchical clustering, and then cutting the resulting dendrogram into neat
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
333 chunks using the dynamicTreeCut package - where each 'chunk' of the dendrogram results in a group of
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
334 features likely to be derived from a single compound. Importantly, this is achieved without looking for
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
335 specific phenomenon (i.e. sodiation), meaning that grouping can be performed on any dataset, whether it
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
336 is positive or negative ionization mode, EI or ESI, LC-MS GC-MS or CE-MS, in-source fragment or complex
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
337 adduction event, and predictable or unpredictable signals.
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
338 </token>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
339
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
340 <token name="@HELP_experiment@">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
341 <![CDATA[
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
342 Create an Experimental Design specification for RAMClustR experiment.
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
343
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
344 Downstream Tools
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
345 +-----------+-----------------------+--------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
346 | Name | Output File | Format |
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
347 +===========+=======================+========+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
348 | RAMClustR | Experiment definition | csv |
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
349 +-----------+-----------------------+--------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
350
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
351 ]]>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
352 </token>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
353 </macros>