Mercurial > repos > recetox > ramclustr

annotate macros.xml @ 4:69e0da4703b5 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit b514d9bf91b62bb06d39e6ceee21d8f18876e12b"
author recetox
date Fri, 04 Feb 2022 08:31:26 +0000
parents 211cd88b5148
children 10ded21d47c0
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3
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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1 <macros>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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2 <token name="@TOOL_VERSION@">1.2.2</token>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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3
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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4 <xml name="creator">
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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5 <creator>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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6 <person
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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7 givenName="Helge"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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8 familyName="Hecht"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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9 url="https://github.com/hechth"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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10 identifier="0000-0001-6744-996X" />
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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11 <person
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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12 givenName="Maksym"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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13 familyName="Skoryk"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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14 url="https://github.com/maximskorik"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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15 identifier="0000-0003-2056-8018" />
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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16 <person
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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17 givenName="Matej"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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18 familyName="Troják"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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19 url="https://github.com/xtrojak"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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20 identifier="0000-0003-0841-2707" />
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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21 <person
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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22 givenName="Martin"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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23 familyName="Čech"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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24 url="https://github.com/martenson"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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25 identifier="0000-0002-9318-1781" />
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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26 <organization
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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27 url="https://www.recetox.muni.cz/"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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28 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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29 name="RECETOX MUNI"/>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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30 </creator>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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31 </xml>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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32
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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33 <xml name="parameters_csv">
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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34 <section name="ms_csv" title="Input MS Data as CSV" expanded="true">
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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35 <param label="ms" name="ms" type="data" format="csv"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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36 help="Features as columns, rows as samples. Column header mz_rt"/>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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37 <param label="idmsms" name="idmsms" type="data" format="csv" optional="true"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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38 help="Optional idMSMS / MSe csv data. same dim and names as ms required"/>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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39 <param label="sample_name_column" name="sample_name_column" type="integer" value="1"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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40 help="Which column from the csv file contains sample names?"/>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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41 <param label="feature_delimiter" name="feature_delimiter" type="text" value="_"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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42 help="Only required if ms input is set! How feature mz and rt are delimited in csv import column header e.g. ='-'"/>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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43 <param label="retention_time_column" name="retention_time_column" type="integer" value="2"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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44 help="Which position in delimited column header represents the retention time (csv only)"/>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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45 <param label="st" name="st" type="float" value="1" help="Sigma t - time similarity decay value.
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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46 A recommended starting point is half the value of your average chromatographic peak width at half max (seconds))."/>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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47 </section>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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48 </xml>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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49
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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50 <xml name="parameters_excluded">
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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51 <param label="MStag" name="MStag" type="text" optional="true"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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52 help="Character string in 'taglocation' to designat MS / MSe files e.g. '01.cdf'"/>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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53 <param label="idMSMStag" name="idMSMStag" type="text" optional="true"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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54 help="Character string in 'taglocation' to designat idMSMS / MSe files e.g. '02.cdf'"/>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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55 <param label="taglocation" name="taglocation" type="text" value="filepaths"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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56 help="'filepaths' by default, 'phenoData[,1]' is another option. refers to xcms slot"/>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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57 </xml>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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58
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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59 <xml name="parameters_required">
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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60 <section name="required" title="Required Parameters" expanded="true">
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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61 <param label="sr" name="sr" type="float" value="0.5" help="Sigma r - correlational similarity decay value"/>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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62 <param label="deepSplit" name="deepSplit" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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63 help="Controls how agressively the HCA tree is cut - see ?cutreeDynamicTree"/>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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64 <param label="blocksize" name="blocksize" type="integer" value="2000"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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65 help="Number of features (scans?) processed in one block =1000,"/>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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66 <param label="mult" name="mult" type="integer" value="5"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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67 help="Internal value, can be used to influence processing speed/ram usage"/>
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68 <param label="hmax" name="hmax" type="float" value="0.3"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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69 help="Precut the tree at this height, default 0.3 - see ?cutreeDynamicTree"/>
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70 <param label="collapse" name="collapse" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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71 help="Reduce feature intensities to spectrum intensities?"/>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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72 <param label="usePheno" name="usePheno" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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73 help="Transfer phenotype data from XCMS object to SpecAbund dataset?"/>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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74 <!--
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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75 Currently not forwarded because the MSP is exported always manually afterwards
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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76 <param label="mspout" name="mspout" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" help="write msp formatted spectra to file?" />
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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77 -->
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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78 <param label="normalize" name="normalize" type="select" display="radio"
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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79 help="Either 'none', 'TIC', 'quantile', or 'batch.qc' normalization of feature intensities. see batch.qc overview in details. ">
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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80 <option value="none" selected="true">none</option>
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81 <option value="TIC">TIC</option>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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82 <option value="quantile">quantile</option>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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83 <option value="batch.qc">batch.qc</option>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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84 </param>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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85 <param label="qc_inj_range" name="qc_inj_range" type="integer" value="20"
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86 help="How many injections around each injection are to be scanned for presence of QC samples when
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87 using batch.qc normalization? A good rule of thumb is between 1 and 3 times the typical
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88 injection span between QC injections. i.e. if you inject QC ever 7 samples, set this to
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89 between 7 and 21. Smaller values provide more local precision but make normalization sensitive
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90 to individual poor outliers (though these are first removed using the boxplot function outlier
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91 detection), while wider values provide less local precision in normalization but better
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92 stability to individual peak areas."/>
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93
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94 <param label="minModuleSize" name="minModuleSize" type="integer" value="2"
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95 help="How many features must be part of a cluster to be returned? default = 2"/>
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96 <param label="linkage" name="linkage" type="select" display="radio" value="average"
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97 help="Hierarchical clustering linkage method - see ?hclust">
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98 <option value="average" selected="true">average</option>
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99 <option value="ward.D">ward.D</option>
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100 <option value="ward.D2">ward.D2</option>
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101 <option value="single">single</option>
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102 <option value="complete">complete</option>
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103 <option value="mcquitty">mcquitty</option>
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104 <option value="median">median</option>
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105 <option value="centroid">centroid</option>
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106 </param>
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107
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108 <param label="mzdec" name="mzdec" type="integer" value="3"
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109 help="Number of decimal places used in printing m/z values"/>
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110 <param label="cor_method" name="cor_method" type="select" display="radio" value="pearson"
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111 help="Which correlational method used to calculate 'r' - see ?cor">
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112 <option value="pearson" selected="true">pearson</option>
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113 <option value="everything">everything</option>
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114 <option value="spearman">spearman</option>
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115 <option value="kendall">kendall</option>
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116 </param>
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117
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118 <param label="rt_only_low_n" name="rt_only_low_n" type="boolean" truevalue="TRUE" falsevalue="FALSE"
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119 checked="true"
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120 help="At low injection numbers, correlational relationships of peak intensities may be unreliable.
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121 By defualt ramclustR will simply ignore the correlational r value and cluster on retention time alone.
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122 If you wish to use correlation with at n less than 5, set this value to FALSE."/>
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123 <param label="replace_zeros" name="replace_zeros" type="boolean" truevalue="TRUE" falsevalue="FALSE"
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124 checked="true"
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125 help="NA, NaN, and Inf values are replaced with zero, and zero values are sometimes returned from
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126 peak peaking. When TRUE, zero values will be replaced with a small amount of noise, with noise level
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127 set based on the detected signal intensities for that feature. "/>
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128 <param label="Merge MSP Files" name="merge_msp" type="boolean" truevalue="TRUE" falsevalue="FALSE"
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129 checked="true" help="Whether to merge all msp in one file or export one msp per spectra"/>
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130 </section>
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131 </xml>
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132
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133 <xml name="parameters_optional_xcms">
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134 <section name="optional" title="Optional Parameters" expanded="false">
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135 <param label="st" name="st" type="float" optional="true" help="Sigma t - time similarity decay value.
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136 A recommended starting point is half the value of your average chromatographic peak width at half max (seconds))."/>
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137 <param label="fftempdir" name="fftempdir" type="text" optional="true"
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138 help="Valid path: if there are file size limitations on the default ff pacakge temp directory -
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139 getOptions('fftempdir') - you can change the directory used as the fftempdir with this option."/>
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140 <param label="maxt" name="maxt" type="integer" optional="true"
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141 help="Maximum time difference to calculate retention similarity for - all values beyond this are assigned similarity of zero"/>
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142 </section>
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143 </xml>
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144
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145 <xml name="parameters_optional_csv">
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146 <section name="optional" title="Optional Parameters" expanded="false">
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147 <param label="fftempdir" name="fftempdir" type="text" optional="true"
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148 help="Valid path: if there are file size limitations on the default ff pacakge temp directory -
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149 getOptions('fftempdir') - you can change the directory used as the fftempdir with this option."/>
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150 <param label="maxt" name="maxt" type="integer" optional="true"
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151 help="Maximum time difference to calculate retention similarity for - all values beyond this are assigned similarity of zero"/>
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152 </section>
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153 </xml>
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154
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155 <xml name="parameters_optional_metadata">
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156 <section name="metadata" title="Optional Metadata" expanded="false">
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157 <param label="metadata" name="batch_order_qc" type="data" format="csv" optional="true"
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158 help="CSV with sample names (or indices, currently not handled) on rows and columns with: batch
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159 number ('batch'), position in sequence ('order') and whether it is a qc sample or not
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160 ('qc' with true/false OR 'sampleType' with 'sample/qc/blank')."/>
4
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161 <param label="Experimental design" name="ExpDes" type="data" format="csv" optional="true" help="Definition of experimental design in CSV format." />
3
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162 </section>
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163 </xml>
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164
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165 <xml name="output_msp">
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166 <collection label="Mass spectra from ${tool.name} on ${on_string}" name="mass_spectra" type="list">
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167 <discover_datasets pattern="__name_and_ext__" directory="spectra" recurse="true" ext="msp"/>
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168 </collection>
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169 </xml>
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170
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171 <xml name="citations">
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172 <citations>
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173 <!-- Example of annotating a citation using a BibTex entry. -->
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174 <citation type="bibtex">
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175 @article{Broeckling2014e,
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176 abstract = {Metabolomic data are frequently acquired using chromatographically coupled mass spectrometry
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177 (MS) platforms. For such datasets, the first step in data analysis relies on feature detection, where a
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178 feature is defined by a mass and retention time. While a feature typically is derived from a single
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179 compound, a spectrum of mass signals is more a more-accurate representation of the mass spectrometric
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180 signal for a given metabolite. Here, we report a novel feature grouping method that operates in an
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181 unsupervised manner to group signals from MS data into spectra without relying on predictability of the
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182 in-source phenomenon. We additionally address a fundamental bottleneck in metabolomics, annotation of MS
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183 level signals, by incorporating indiscriminant MS/MS (idMS/MS) data implicitly: feature detection is
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184 performed on both MS and idMS/MS data, and feature-feature relationships are determined simultaneously
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185 from the MS and idMS/MS data. This approach facilitates identification of metabolites using in-source MS
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186 and/or idMS/MS spectra from a single experiment, reduces quantitative analytical variation compared to
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187 single-feature measures, and decreases false positive annotations of unpredictable phenomenon as novel
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188 compounds. This tool is released as a freely available R package, called RAMClustR, and is sufficiently
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189 versatile to group features from any chromatographic-spectrometric platform or feature-finding software.
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190 {\textcopyright} 2014 American Chemical Society.},
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191 author = {Broeckling, C. D. and Afsar, F. A. and Neumann, S. and Ben-Hur, A. and Prenni, J. E.},
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192 doi = {10.1021/ac501530d},
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193 issn = {15206882},
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194 journal = {Analytical Chemistry},
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195 number = {14},
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196 pages = {6812--6817},
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197 pmid = {24927477},
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198 title = {{RAMClust: A novel feature clustering method enables spectral-matching-based annotation for
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199 metabolomics data}},
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200 volume = {86},
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201 year = {2014}
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202 }
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203 </citation>
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204 </citations>
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205 </xml>
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206
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207 <token name="@HELP@">
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208 <![CDATA[
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209 Documentation
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210 For documentation on the tool see https://github.com/cbroeckl/RAMClustR/blob/master/vignettes/RAMClustR.Rmd
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211
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212 Upstream Tools
4
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213 +------------------------------+-------------------------------+----------------------+---------------------+
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214 | Name | Output File | Format | Parameter |
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215 +==============================+===============================+======================+=====================+
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216 | xcms | xset.fillPeaks.RData | rdata.xcms.fillpeaks | xcmsObj |
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217 +------------------------------+-------------------------------+----------------------+---------------------+
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218 | RAMClustR define experiment | Table with experiment details | csv | Experimental design |
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219 +------------------------------+-------------------------------+----------------------+---------------------+
3
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220
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221 The tool takes an **xcmsSet** object as input and extracts all relevant information.
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222
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223 +-------+------------------------+--------+------------+
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224 | Name | Output File | Format | Parameter |
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225 +=======+========================+========+============+
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226 | ??? | Feature Table with MS1 | csv | ms |
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227 +-------+------------------------+--------+------------+
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228 | ??? | Feature Table with MS2 | csv | idmsms |
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229 +-------+------------------------+--------+------------+
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230
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231 Alternatively, the tool takes a **csv** table as input which has to fulfill the following requirements
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232
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233 (1) no more than one sample (or file) name column and one feature name row;
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234 (2) feature names that contain the mass and retention times, separated by a constant delimiter; and
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235 (3) features in columns and samples in rows.
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236
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237 Downstream Tools
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238 +---------+--------------+----------------------+
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239 | Name | Output File | Format |
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240 +=========+==============+======================+
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241 | matchMS | Mass Spectra | collection (tgz/msp) |
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242 +---------+--------------+----------------------+
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243
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244 @GENERAL_HELP@
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245 ]]>
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246 </token>
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247
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248 <token name="@GENERAL_HELP@">
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249 Background
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250 Metabolomics
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251 Metabolomics is frequently performed using chromatographically coupled mass spectrometry, with gas
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252 chromatography, liquid chromatography, and capillary electrophoresis being the most frequently utilized
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253 methods of separation. The coupling of chromatography to mass spectrometry is enabled with an
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254 appropriate ionization source - electron impact (EI) for gas phase separations and electrospray
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255 ionization (ESI) for liquid phase separations. XCMS is a commonly used tool to detect all the signals
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256 from a metabolomics dataset, generating aligned features, where a feature is represented by a mass and
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257 retention time. Each feature is presumed to derive from a single compound. However, each compound is
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258 represented by several features. With any ionization method, isotopic peaks will be observed reflective
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259 of the elemental composition of the analyte. In EI, fragmentation is a byproduct of ionization, and has
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260 driven the generation of large mass spectral libraries. In ESI, in-source fragmentation frequently
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261 occurs, the magnitude of which is compound dependent, with more labile compounds being more prone to
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262 in-source fragmentation. ESI can also product multiple adduct forms (protonated, potassiated, sodiated,
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263 ammoniated...), and can produce multimers (i.e. [2M+H]+, [3M+K]+, etc) and multiple charged species
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264 ([M+2H]++). This can become further complicated by considering combinations of these phenomena. For
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265 example [2M+3H]+++ (triply charged dimer) or an in-source fragment of a dimer.
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266
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267 RAMClustR approach
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268 RAMClustR was designed to group features designed from the same compound using an approach which is
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269 __1.__ unsupervised, __2.__ platform agnosic, and __3.__ devoid of curated rules, as the depth of
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270 understanding of these processes is insufficent to enable accurate curation/prediction of all phenomenon
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271 that may occur. We acheive this by making two assumptions. The first is that two features derived
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272 from the same compound with have (approximately) the same retention time. The second is that two
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273 features derived from the same compound will have (approximately) the same quantitative trend across
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274 all samples in the xcms sample set. From these assumptions, we can calculate a retention time
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275 similarity score and a correlational similarity score for each feature pair. A high similarity score
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276 for both retention time and correlation indicates a strong probability that two features derive from
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277 the same compound. Since both conditions must be met, the product of the two similarity scores provides
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278 the best approximatio of the total similarity score - i.e. a feature pair with retention time similarity
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279 of 1 and correlational similarity of 0 is unlikely to derive from one compound - 1 x 0 = 0, the final
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280 similarity score is zero, indicating the two features represent two different compounds. Similarly, a
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281 feature pair with retention time similarity of 0 and correlational similarity of 1 is unlikely to derive
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282 from one compound - 0 x 1 = 0. Alternatively - a feature pair with retention time similarity of 1 and
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283 correlational similarity of 1 is likely to derive from one compound - 1 x 1 = 1.
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284
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285 The RAMClustR algorithm is built on creating similarity scores for all pairs of features, submitting
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286 this score matrix for heirarchical clustering, and then cutting the resulting dendrogram into neat
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287 chunks using the dynamicTreeCut package - where each 'chunk' of the dendrogram results in a group of
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288 features likely to be derived from a single compound. Importantly, this is acheived without looking for
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289 specific phenomenon (i.e. sodiation), meaning that grouping can be performed on any dataset, whether it
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290 is poisitive or negative ionization mode, EI or ESI, LC-MS GC-MS or CE-MS, in-source fragment or complex
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291 adduction event, and predictable or unpredictable signals.
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292 </token>
4
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293
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294 <token name="@HELP_experiment@">
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295 <![CDATA[
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296 Create an Experimental Design specification for RAMClustR experiment.
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297
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298 Downstream Tools
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299 +-----------+-----------------------+--------+
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300 | Name | Output File | Format |
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301 +===========+=======================+========+
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302 | RAMClustR | Experiment definition | csv |
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303 +-----------+-----------------------+--------+
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304
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305 ]]>
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306 </token>
3
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307 </macros>