annotate msclust2.0.1.xml @ 0:9d5f4f5f764b

Initial commit to toolshed
author pieter.lukasse@wur.nl
date Thu, 16 Jan 2014 13:10:00 +0100
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
1 <tool name="MsClust" id="msclust2" version="2.0.1">
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
2 <description>Extracts fragmentation spectra from aligned data</description>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
3 <!--
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
4 For remote debugging start you listener on port 8000 and use the following as command interpreter:
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
6 //////////////////////////
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
7
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
8 TODO in command below: add conditionals according to options of using or NOT the tolerances/thresholds from previous steps
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
9 -->
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
10 <command interpreter="java -jar ">
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
11 MsClust.jar
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
12 -peaksFileName $inputPeaks
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
13 -dataType $dataType
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
14 -imputationMethod $imputationMethod.type
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
15 #if $imputationMethod.type == "valueRange"
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
16 -rangeUpperLimit $imputationMethod.rangeUpperLimit
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
17 #end if
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
18 -plInputFormat "metalign"
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
19 -potDensFuncType $potDensFuncType.type
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
20 -centerSelectionType $centerSelectionType.type
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
21 -clusteringType $clusteringType.type
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
22 -neighborhoodWindowSize $potDensFuncType.pdf_neighborhoodWindowSize
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
23 -clusterSearchStopCriterium $centerSelectionType.cs_stop_criterion
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
24 -pearsonDistTreshold $potDensFuncType.pdf_pears_treshold
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
25 -pearsonTresholdConfidence $potDensFuncType.pdf_pears_conf
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
26 -pearsonPDReductionThreshold $centerSelectionType.cs_pears_pd_reductionTreshold
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
27 -pearsonPDReductionSlope $centerSelectionType.cs_pears_pd_reductionSlope
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
28 -scanDistTol $potDensFuncType.pdf_scan_toler
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
29 -scanDistanceConfidence $potDensFuncType.pdf_scan_conf
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
30 -centrotypesOut $centrotypesOut
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
31 -simOut $simOut
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
32 -micOut $micOut
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
33 -mspOut $mspOut
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
34 -classOut $classOut
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
35 -outReport $htmlReportFile
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
36 -outReportPicturesPath $htmlReportFile.files_path
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
37 #if $clusteringType.type == "fuzzyCMeans"
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
38 -fcmMembershipWeightingExponent $clusteringType.fcmMembershipWeightingExponent
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
39 -fcmStopCriterion $clusteringType.fcmStopCriterion
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
40 -fcmCorrelationWeight $clusteringType.fcmCorrelationWeight
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
41 -fcmFinalAssemblyType $clusteringType.finalClusterAssembly.type
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
42 #if $clusteringType.finalClusterAssembly.type == "membershipBased"
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
43 -fcmMembershipCutoff $clusteringType.finalClusterAssembly.fcmMembershipCutoff
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
44 #end if
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
45 #end if
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
46 -verbose "false"
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
47 #if $advancedSettings.settings == True
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
48 -advancedSettings YES
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
49 -saturationLimit $advancedSettings.saturationLimit
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
50 -sampleSelectionSortType $advancedSettings.sampleSelectionSortType
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
51 -simSelectionAlgorithm $advancedSettings.simSelectionAlgorithm
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
52 -simMassFilter "$advancedSettings.simMassFilter"
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
53 -simMembershipThreshold $advancedSettings.simMembershipThreshold
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
54 -simSaturationThreshold $advancedSettings.simSaturationThreshold
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
55 -simAbsenseThreshold $advancedSettings.simAbsenseThreshold
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
56 -micMembershipThreshold $advancedSettings.micMembershipThreshold
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
57 -peakIntensityCorrectionAlgorithm $advancedSettings.peakIntensityCorrectionAlgorithm
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
58 #else
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
59 -advancedSettings YES
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
60 -sampleSelectionSortType SIM_INTENSITY
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
61 -peakIntensityCorrectionAlgorithm CORRELATION_BASED
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
62 #end if
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
63
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
64 </command>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
65 <inputs>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
66 <!-- <param name="rankingWeightConfig" type="text" area="true" size="11x70" label="NB - TEST VERSION"
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
67 value="VERSION BEING TESTED AT THIS MOMENT...NOT READY FOR USE..."/>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
68 -->
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
69 <param name="inputPeaks" type="data" format="txt" label="Ion-wise aligned data (e.g. MetAlign output data)" />
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
70 <param name="dataType" type="select" size="30" label="Data type">
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
71 <option value="gcms" selected="true">GC-MS</option>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
72 <option value="lcms">LC-MS</option>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
73 </param>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
74 <conditional name="imputationMethod">
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
75 <param name="type" type="select" size="30" label="Select the approach used for imputing missing values (optional)" help="select how you generated the values to fill in the data gaps">
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
76 <option value="none" >none</option>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
77 <option value="metot" selected="true">MeTot</option>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
78 <option value="valueRange">Values range</option>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
79 </param>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
80 <when value="valueRange">
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
81 <param name="rangeUpperLimit" type="integer" size="10" value="0" label="Range upper limit" help="values up to this limit will be considered 'generated' values" />
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
82 </when>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
83 </conditional>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
84 <conditional name="potDensFuncType">
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
85 <param name="type" type="select" size="30" label="Select PD function type =====================================================">
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
86 <option value="original" selected="true">Original</option>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
87 </param>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
88 <when value="original">
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
89 <param name="pdf_neighborhoodWindowSize" type="integer" size="10" value="200" label="Effective Peaks" />
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
90 <param name="pdf_scan_toler" type="float" size="10" value="10" label="Peak Width, in scans" />
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
91 <param name="pdf_scan_conf" type="float" size="10" value="80" label="Peak Width confidence (0.0 to 99.99)" help="example: 0[no confidence]...50[good guess]...99.9[quite certain])" />
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
92 <param name="pdf_pears_treshold" type="float" size="10" value="0.8" label="Correlation threshold (0.0 - 1.0)" />
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
93 <param name="pdf_pears_conf" type="float" size="10" value="98.0" label="Correlation threshold confidence (0.0 to 99.99)" help="example: 0[no confidence]...50[good guess]...99.9[quite certain])" />
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
94 </when>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
95 </conditional>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
96 <conditional name="centerSelectionType">
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
97 <param name="type" type="select" label="Initial Centers selection type ==================================================" >
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
98 <option value="original" selected="true">Original - Subtractive potential reductions with stop criterion and REUSE tolerances (from PD function)</option>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
99 </param>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
100 <when value="original">
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
101 <param name="cs_pears_pd_reductionTreshold" type="float" size="10" value="0.8" label="Potential Density reduction (0.0 - 1.0)" />
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
102 <param name="cs_pears_pd_reductionSlope" type="float" size="10" value="0.01" label="Potential Density reduction softness " />
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
103 <param name="cs_stop_criterion" type="float" size="10" value="2" label="Stop Criterion " />
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
104 </when>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
105 </conditional>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
106 <conditional name="clusteringType">
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
107 <param name="type" type="select" label="Classify using ===========================================================">
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
108 <option value="original" selected="true">Original - Fuzzy clustering, keep original centers and REUSE (scan distance) tolerances</option>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
109 <option value="fuzzyCMeans">(experimental) Fuzzy C-Means - Fuzzy clustering, optimize centers</option>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
110 </param>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
111 <when value="original">
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
112 <!-- nothing -->
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
113 </when>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
114 <when value="originalNewTol">
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
115 <param name="clust_scan_toler" type="float" size="10" value="10" label="Peak Width, in scans" />
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
116 <param name="clust_scan_slope" type="float" size="10" value="2" label="Peak Width margin softness" />
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
117 </when>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
118 <when value="fuzzyCMeans">
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
119 <param name="fcmMembershipWeightingExponent" type="float" size="10" value="2.0" label="Membership Weighting Exponent" help="Influences cluster center repositioning in the iterations 1.1 (exploratory) to around 3.0 (conservative)" />
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
120 <param name="fcmStopCriterion" type="float" size="10" value="0.05" label="Stop Criterion" help="When convergence is 'reached' (e.g. 0.05 means memberships only changed with 5% in last iteration)" />
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
121 <param name="fcmCorrelationWeight" type="float" size="10" value="2" label="Correlation weight factor" help="Increase this if you think the correlation is reliable (e.g. you have a high number of samples)" />
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
122 <conditional name="finalClusterAssembly">
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
123 <param name="type" type="select" label="Final cluster assembly" >
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
124 <option value="original" selected="true">Original - distance based</option>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
125 <option value="membershipBased">Membership based</option>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
126 </param>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
127 <when value="membershipBased">
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
128 <param name="fcmMembershipCutoff" type="select" label="Maximum allowed peak overlap" >
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
129 <option value="0.05" >~7 clusters</option>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
130 <option value="0.10" >~5 clusters</option>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
131 <option value="0.20" >~3 clusters</option>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
132 </param>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
133 </when>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
134 <when value="original">
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
135 <!-- nothing -->
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
136 </when>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
137 </conditional>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
138 </when>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
139 </conditional>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
140
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
141 <param name="summaryReport" type="boolean" checked="true" label="Generate summary report" help="NB: this will increase the processing time (in some cases up to a few extra minutes)"/>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
142
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
143 <conditional name="advancedSettings">
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
144 <param name="settings" type="boolean" truevalue="Yes" falsevalue="No" checked="false" label="Advanced settings ========================================================"/>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
145 <when value="Yes">
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
146 <param name="saturationLimit" optional="true" type="integer" size="10" label="Saturation limit (optional)" help="fill in if you have saturation problems in your data" />
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
147 <param name="sampleSelectionSortType" type="select" label="Sample selection scheme for spectrum peak intensity correction algorithm (optional/experimental)" help="The intensity values to use to select the samples for each cluster/metabolite in which it is most intense/abundant. These samples are used in the peak intensity correction (see parameter below). Use this option to try to avoid samples that have insufficient signal or saturation." >
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
148 <option value="None">None</option>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
149 <!-- in order of best FORWARD scoring when tested on /test/data/report_test_sets/(P2) Relative peak heights in spectra/Input (Test set 1) -->
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
150 <option value="SIM_INTENSITY" selected="true">SIM intensities</option>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
151 <option value="MAX_INTENSITY">Maximum intensities</option>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
152 <option value="CENTROTYPE_INTENSITY">Centrotype peak intensities</option>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
153 <option value="MIC_INTENSITY">MIC intensities</option>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
154 </param>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
155 <param name="peakIntensityCorrectionAlgorithm" type="select" label="Spectrum peak intensity correction algorithm (optional/experimental)" help="Whether spectrum peak heights should be adjusted according to their membership to the cluster or to their correlation to the cluster's centrotype ion" >
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
156 <option value="MEMBERSHIP_BASED">Membership based (msclust 1.0 mode)</option>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
157 <option value="CORRELATION_BASED" selected="true">Correlation based</option>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
158 </param>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
159 <param name="simSelectionAlgorithm" type="select" label="SIM selection algorithm (experimental)" help="Set this if you want to deviate from the standard which is: allow shared SIM peaks for GC-MS data, and force unique SIM peaks for LC-MS data">
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
160 <option value="" selected="true"></option>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
161 <option value="uniqueSIM">Unique SIM peak</option>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
162 <option value="sharedSIM">Shared SIM peak</option>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
163 </param>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
164 <param name="simMassFilter" type="text" optional="true" size="30" label="SIM mass exclusion list" help="Comma-separated list of masses NOT to use as SIM peaks. E.g. '73,147,...' " />
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
165 <param name="simMembershipThreshold" optional="true" type="float" size="10" label="SIM membership threshold" help="Minimum membership a peak should have to qualify as a SIM candidate. E.g. 0.8 " />
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
166 <param name="simSaturationThreshold" optional="true" type="float" size="10" label="SIM saturation threshold (%)" help="Maximum % of samples in which a SIM candidate peak may be saturated. If the candidate peak exceeds this threshold, then another peak is chosen. If no peak can be found this criteria, mass 0 is reported" />
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
167 <param name="simAbsenseThreshold" optional="true" type="float" size="10" label="SIM absence threshold (%)" help="Maximum % of samples in which a SIM candidate peak may be absent. If the candidate peak exceeds this threshold, then another peak is chosen. If no peak can be found meeting this criteria, mass 0 is reported" />
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
168
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
169 <param name="micMembershipThreshold" optional="true" type="float" size="10" label="MIC membership threshold" help="Minimum membership a peak should have to be counted in the MIC sum. E.g. 0.8 " />
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
170
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
171 </when>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
172 </conditional>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
173
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
174
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
175 </inputs>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
176 <outputs>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
177 <data name="centrotypesOut" format="msclust.csv" label="${tool.name} on ${on_string} - centrotypes file"/>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
178 <data name="simOut" format="msclust.csv" label="${tool.name} on ${on_string} - SIM file"/>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
179 <data name="micOut" format="msclust.csv" label="${tool.name} on ${on_string} - MIC file"/>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
180 <data name="mspOut" format="msp" label="${tool.name} on ${on_string} - SPECTRA file"/>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
181 <data name="classOut" format="msclust.csv" label="${tool.name} on ${on_string} - Classification file"/>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
182 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - HTML report">
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
183 <!-- If the expression is false, the file is not created -->
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
184 <filter>( summaryReport == True )</filter>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
185 </data>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
186 </outputs>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
187 <tests>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
188 <!-- find out how to use -->
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
189 </tests>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
190 <help>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
191
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
192 <!-- see also http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html#hyperlink-targets -->
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
193
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
194 .. class:: infomark
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
195
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
196 This tool extracts spectra from ion-wise aligned MS(/MS) results. It uses expression profiles and
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
197 retention times of the putative ions to cluster them. Each cluster is then used to generate
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
198 one spectrum containing the clustered ions (peaks).
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
199
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
200 .. image:: $PATH_TO_IMAGES/msclust_summary.png
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
201
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
202
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
203 -----
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
204
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
205 **Output**
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
206
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
207 This tools returns a number of ouptut files and a small report.
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
208
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
209 **Parameters index**
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
210
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
211
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
212 *Select the approach used for imputing missing values:* only select this if you have used a specific method to
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
213 fill in the data gaps in the input file. One example is replacing zero values by some randomly generated low value.
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
214 If MeTot is chosen, then a value is considered generated if: the value contains a dot '.' and some number
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
215 other than 0 (zero) after the dot.
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
216
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
217 *Effective Peaks:* Neighborhood window size to consider when calculating density. Smaller values increase
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
218 performance but are less reliable.
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
219
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
220 *Peak Width, in scans:* Scan window width of scans to consider 'close'. One can see this as the
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
221 'tolerated variation in scans' for the apex positions of the fragment peaks composing a cluster.
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
222 Note: if MetAlign was used, this is the variation *after* pre-processing by MetAlign.
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
223
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
224 *Peak Width confidence:* The higher the confidence, the stricter the threshold.
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
225
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
226 *Correlation threshold (0.0 - 1.0):* Tolerance center for pearson distance calculation. The higher this value,
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
227 the higher the correlation between 2 items has to be for them to be considered 'close'.
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
228
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
229 *Correlation threshold confidence:* The higher the confidence, the stricter the threshold. `More...`__
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
230
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
231 *Potential Density reduction (0.0 - 1.0):* Reduction tolerance center for pearson distance calculation.
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
232 The higher this value, the less the low correlated items get reduced, getting a chance to form a cluster of their own.
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
233
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
234 *Potential Density reduction softness:* Reduction curve slope for pearson distance tolerance. Lower
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
235 values = stricter separation at the value determined in 'Potential Density reduction' above
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
236 (TODO review this comment).
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
237
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
238 *Stop Criterion:* When to stop reducing and looking for new clusters. Lower values = more iterations
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
239
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
240 .. __: javascript:window.open('$PATH_TO_IMAGES/confidence_and_slope_params_explain.png','popUpWindow','height=700,width=800,left=10,top=10,resizable=yes,scrollbars=yes,toolbar=yes,menubar=no,location=no,directories=no,status=yes')
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
241
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
242
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
243 -----
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
244
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
245 **Output files described below**
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
246
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
247 -----
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
248
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
249 *SPECTRA:* this file can be submitted to NIST for identification of the spectra.
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
250
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
251 `Click here for more details on the Sample selection and Spectrum peak intensity correction algorithm parameters related to SPECTRA generation`_
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
252
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
253 .. _Click here for more details on the Sample selection and Spectrum peak intensity correction algorithm parameters related to SPECTRA generation: javascript:window.open('$PATH_TO_IMAGES/sample_sel_and_peak_height_correction.png','popUpWindow','height=700,width=800,left=10,top=10,resizable=yes,scrollbars=yes,toolbar=yes,menubar=no,location=no,directories=no,status=yes')
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
254
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
255 -----
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
256
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
257 *MIC:* stands for Measured Ions Count -> it contains, for each cluster, the sum of the ion count
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
258 values (corrected by their membership) for all MEASURED cluster ions in the given sample.
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
259
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
260 The MIC for a **cluster i** in **sample s**, where **cluster i** has **n** members is thus:
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
261
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
262 sum ( [intensity of member n in **sample s**] x [membership value of member n in **cluster i** ] )
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
263
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
264 -----
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
265
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
266 *SIM:* stands for Selective Ion Mode -> it contains, for each cluster, the intensity values of the
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
267 most representative member ion peak of this cluster. The most representative member peak is the one with the
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
268 highest membership*average_intensity. This definition leads to conflicts as a peak can have a
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
269 membership in two or more clusters. The assignment of a SIM peak to a cluster depends on
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
270 the configured data type (LC or GC-MS). NB: this can be overruled in the "advanced settings":
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
271
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
272 (1) LC-MS SIM: select SIM peak only once and for the centrotype in which this specific mass has its
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
273 highest membership; for neighboring centrotypes use its "second best SIM", etcetera. In other words,
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
274 if the SIM peak has been identified as the SIM in more than 1 cluster, assign as SIM to the cluster
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
275 with highest membership. Continue searching for other SIM peaks to assign to the other clusters until
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
276 all ambiguities are solved.
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
277
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
278 (2) GC-MS SIM: the SIM peak can be "shared" by multiple clusters. However, the intensity values are corrected
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
279 by the membership value of the peak in the cluster in case the SIM peak is "shared". If the SIM peak is not
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
280 "shared" then the "raw" intensity values of the SIM peak are recorded in the SIM file.
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
281
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
282 `Click here for more details on the SIM output file`_
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
283
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
284 .. _Click here for more details on the SIM output file: javascript:window.open('$PATH_TO_IMAGES/sample_SIM.png','popUpWindow','height=700,width=800,left=10,top=10,resizable=yes,scrollbars=yes,toolbar=yes,menubar=no,location=no,directories=no,status=yes')
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
285
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
286
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
287
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
288 </help>
9d5f4f5f764b Initial commit to toolshed
pieter.lukasse@wur.nl
parents:
diff changeset
289 </tool>