ramclustr: macros.xml annotate

annotate macros.xml @ 9:d70dd1d6ac4d draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e

author	recetox
date	Wed, 17 Apr 2024 07:51:23 +0000
parents	09cabbc3d12d
children	2d94da58904b

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) < 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 < 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 > rsq.cut will be adjusted. also requires p values < 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."/>
9 d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	187 <param label="Quality control" name="quality_control" type="boolean" truevalue="TRUE" falsevalue="FALSE"
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	188 checked="false"
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	189 help="Add graph to Rplots.pdf output which contains summarize quality control for clustering and for quality
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	190 control sample variation based on compound ($SpecAbund) and feature ($MSdata and $MSMSdata, if present)."/>
0 36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	191 <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	192 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	193 </section>
9 d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	194
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	195 <section name="filtering" title="Filtering">
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	196 <conditional name="feature_filter_blanks">
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	197 <param label="Filter blanks" name="filter_blanks" type="select"
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	198 help="Is used to remove features which are found at similar intensity in blank samples">
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	199 <option value="FALSE" selected="true">FALSE</option>
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	200 <option value="TRUE">TRUE</option>
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	201 </param>
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	202 <when value="TRUE">
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	203 <param label="qc tag" name="qc_tag" type="text" value="QC"
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	204 help="Character vector of length one or two. If length is two, enter search string and factor name in $phenoData slot
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	205 (i.e. c('QC', 'sample.type'). If length one (i.e. 'QC'), will search for this string in the 'sample.names' slot by default.
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	206 Default is 'QC'"/>
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	207 <param label="blank tag" name="blank_tag" type="text" value="blank"
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	208 help="See 'qc tag' , but for blanks to use as background. Default is 'blank'"/>
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	209 <param label="signal to noise (sn)" name="sn" type="integer" value="3"
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	210 help="Numeric defines the ratio for 'signal'. i.e. sn = 3 indicates that signal intensity must be 3 fold higher in sample than in blanks,
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	211 on average, to be retained. Default is '3'"/>
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	212 <param label="Remove blanks" name="remove_blanks" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true"
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	213 help="TRUE by default. This removes any recognized blanks samples from the MSdata and MSMSdata sets after they are used to filter
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	214 contaminant features."/>
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	215 </when>
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	216 <when value="FALSE"></when>
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	217 </conditional>
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	218
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	219 <conditional name="feature_filter_cv">
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	220 <param label="Filter cv" name="filter_cv" type="select"
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	221 help="Extractor for xcms objects in preparation for clustering. This function offers normalization
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	222 by total extracted ion signal. It is recommended to first run 'Filter blanks' to remove non-sample derived signal">
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	223 <option value="FALSE" selected="true">FALSE</option>
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	224 <option value="TRUE">TRUE</option>
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	225 </param>
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	226 <when value="TRUE">
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	227 <param label="qc tag" name="qc_tag" type="text" value="QC"
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	228 help="Character vector of length one or two. If length is two, enter search string and factor name in $phenoData slot
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	229 (i.e. c('QC', 'sample.type'). If length one (i.e. 'QC'), will search for this string in the 'sample.names' slot by default.
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	230 Default is 'QC'"/>
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	231 <param label="Max cv" name="max_cv" type="float" value="0.5" help="Numeric maximum allowable cv for any feature. Default = 0.5."/>
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	232 </when>
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	233 <when value="FALSE"></when>
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	234 </conditional>
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	235 </section>
0 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 <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	239 <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	240 <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	241 <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	242 </collection>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	243 <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	244 <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	245 </data>
9 d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	246 <data format="pdf" name="pdf_plot" from_work_dir="Rplots.pdf" label="PDF plot.">
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	247 <filter>extras['quality_control'] or filtering['feature_filter_cv']['filter_cv'] == "TRUE"</filter>
d70dd1d6ac4d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e recetox parents: 7 diff changeset	248 </data>
0 36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	249 </xml>
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 <xml name="citations">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	252 <citations>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	253 <!-- 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	254 <citation type="bibtex">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	255 @article{Broeckling2014e,
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	256 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	257 (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	258 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	259 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	260 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	261 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	262 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	263 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	264 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	265 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	266 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	267 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	268 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	269 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	270 {\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	271 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	272 doi = {10.1021/ac501530d},
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	273 issn = {15206882},
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	274 journal = {Analytical Chemistry},
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	275 number = {14},
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	276 pages = {6812--6817},
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	277 pmid = {24927477},
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	278 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	279 metabolomics data}},
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	280 volume = {86},
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	281 year = {2014}
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	282 }
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	283 </citation>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	284 </citations>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	285 </xml>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	286
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	287 <token name="@HELP@">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	288 <![CDATA[
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	289 Documentation
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	290 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	291
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	292 Upstream Tools
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 \| 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	295 +==============================+===============================+======================+=====================+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	296 \| 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	297 +------------------------------+-------------------------------+----------------------+---------------------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	298 \| 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	299 +------------------------------+-------------------------------+----------------------+---------------------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	300
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	301 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	302
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	303 +-------+------------------------+--------+------------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	304 \| 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	305 +=======+========================+========+============+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	306 \| ??? \| 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	307 +-------+------------------------+--------+------------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	308 \| ??? \| 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	309 +-------+------------------------+--------+------------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	310
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	311 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	312
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	313 (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	314 (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	315 (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	316
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	317 +----------------------+-------------------+-------------------+--------------------+--------------------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	318 \| 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	319 +======================+===================+===================+====================+====================+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	320 \| 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	321 +----------------------+-------------------+-------------------+--------------------+--------------------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	322 \| 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	323 +----------------------+-------------------+-------------------+--------------------+--------------------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	324 \| 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	325 +----------------------+-------------------+-------------------+--------------------+--------------------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	326 \| 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	327 +----------------------+-------------------+-------------------+--------------------+--------------------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	328
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	329
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	330 Downstream Tools
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	331 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	332
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	333 +---------+--------------+----------------------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	334 \| Name \| Output File \| Format \|
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	335 +=========+==============+======================+
6 9b716db0a786 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit f79a5b51599254817727bc9028b9797ea994cb4e recetox parents: 5 diff changeset	336 \| 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	337 +---------+--------------+----------------------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	338
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	339 @GENERAL_HELP@
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	340 ]]>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	341 </token>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	342
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	343 <token name="@GENERAL_HELP@">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	344 Background
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	345 Metabolomics
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	346 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	347 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	348 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	349 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	350 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	351 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	352 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	353 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	354 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	355 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	356 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	357 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	358 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	359 ([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	360 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	361
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	362 RAMClustR approach
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	363 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	364 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	365 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	366 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	367 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	368 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	369 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	370 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	371 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	372 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	373 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	374 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	375 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	376 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	377 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	378 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	379
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	380 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	381 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	382 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	383 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	384 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	385 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	386 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	387 </token>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	388
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	389 <token name="@HELP_experiment@">
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	390 <![CDATA[
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	391 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	392
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	393 Downstream Tools
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	394 +-----------+-----------------------+--------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	395 \| Name \| Output File \| Format \|
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	396 +===========+=======================+========+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	397 \| RAMClustR \| Experiment definition \| csv \|
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	398 +-----------+-----------------------+--------+
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	399
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	400 ]]>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	401 </token>
36104baf75da "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" recetox parents: diff changeset	402 </macros>

Mercurial > repos > recetox > ramclustr

annotate macros.xml @ 9:d70dd1d6ac4d draft