Mercurial > repos > eschen42 > w4mkmeans
annotate w4mkmeans.xml @ 1:02cafb660b72 draft
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit f600ce8a783df16e49272341dce0fc6bbc299b0a
author | eschen42 |
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date | Wed, 09 Aug 2017 18:06:55 -0400 |
parents | 6ccbe18131a6 |
children | c415b7dc6f37 |
rev | line source |
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1
02cafb660b72
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit f600ce8a783df16e49272341dce0fc6bbc299b0a
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1 <tool id="w4mkmeans" name="w4mKmeans" version="0.98.3"> |
02cafb660b72
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit f600ce8a783df16e49272341dce0fc6bbc299b0a
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2 <description>Calculate K-means for W4M dataMatrix features or samples</description> |
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6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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3 |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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4 <requirements> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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5 <requirement type="package" version="3.3.2">r-base</requirement> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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6 <requirement type="package" version="1.1_4">r-batch</requirement> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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7 </requirements> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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8 |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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9 <stdio> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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10 <exit_code range="1:" level="fatal" /> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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11 </stdio> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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12 |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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13 |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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14 <command detect_errors="aggressive"><![CDATA[ |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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15 Rscript $__tool_directory__/w4mkmeans_wrapper.R |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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16 tool_directory $__tool_directory__ |
1
02cafb660b72
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit f600ce8a783df16e49272341dce0fc6bbc299b0a
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17 algorithm '$algorithm' |
02cafb660b72
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit f600ce8a783df16e49272341dce0fc6bbc299b0a
eschen42
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18 categorical_prefix '$categoricalPrefix' |
0
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
eschen42
parents:
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19 data_matrix_path '$dataMatrix_in' |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
eschen42
parents:
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20 iter_max '$iter_max' |
1
02cafb660b72
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit f600ce8a783df16e49272341dce0fc6bbc299b0a
eschen42
parents:
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21 kfeatures '$kfeatures' |
02cafb660b72
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit f600ce8a783df16e49272341dce0fc6bbc299b0a
eschen42
parents:
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22 ksamples '$ksamples' |
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6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
eschen42
parents:
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23 nstart '$nstart' |
1
02cafb660b72
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit f600ce8a783df16e49272341dce0fc6bbc299b0a
eschen42
parents:
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24 sampleMetadata_out '$sampleMetadata_out' |
02cafb660b72
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit f600ce8a783df16e49272341dce0fc6bbc299b0a
eschen42
parents:
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25 sample_metadata_path '$sampleMetadata_in' |
0
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
eschen42
parents:
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26 scores_out '$scores_out' |
1
02cafb660b72
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit f600ce8a783df16e49272341dce0fc6bbc299b0a
eschen42
parents:
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27 slots "\${GALAXY_SLOTS:-1}" |
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6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
eschen42
parents:
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28 variableMetadata_out '$variableMetadata_out' |
1
02cafb660b72
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit f600ce8a783df16e49272341dce0fc6bbc299b0a
eschen42
parents:
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29 variable_metadata_path '$variableMetadata_in' |
0
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
eschen42
parents:
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30 ; echo exit code $? |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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31 ]]></command> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
eschen42
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32 |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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33 <inputs> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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34 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, separator: tab" /> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
eschen42
parents:
diff
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35 <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata columns, separator: tab" /> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
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36 <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata columns, separator: tab" /> |
1
02cafb660b72
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit f600ce8a783df16e49272341dce0fc6bbc299b0a
eschen42
parents:
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37 <param name="categoricalPrefix" label="prefix for cluster names " type="text" value="k" help="[categorical_prefix] Some tools require non-numeric values to discern categorical data; e.g., enter 'k' here to prepend 'k' to cluster numbers in the output; default 'k'." /> |
0
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
eschen42
parents:
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38 <param name="ksamples" label="K value(s) for samples" type="text" value = "0" help="[ksamples] Single K or comma-separated Ks for samples, or 0 for none." /> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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39 <param name="kfeatures" label="K value(s) for features" type="text" value = "0" help="[kfeatures] Single K or comma-separated Ks for features (variables), or 0 for none." /> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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40 <param name="iter_max" label="Max number of iterations" type="text" value = "10" help="[iter_max] The maximum number of iterations allowed; default 10." /> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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parents:
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41 <param name="nstart" label="Number of random sets" type="text" value = "1" help="[nstart] How many random sets should be chosen; default 1." /> |
1
02cafb660b72
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit f600ce8a783df16e49272341dce0fc6bbc299b0a
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42 <param name="algorithm" label="Algorithm for clustering" type="select" value = "Hartigan-Wong" help="[algorithm] K-means clustering algorithm, default 'Hartigan-Wong'; alternatives 'Lloyd', 'MacQueen'; 'Forgy' is a synonym for 'Lloyd', see stats::kmeans reference for further info."> |
0
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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43 <option value="Forgy">Forgy</option> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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44 <option value="Hartigan-Wong" selected="True">Hartigan-Wong</option> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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45 <option value="Lloyd">Lloyd</option> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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46 <option value="MacQueen">MacQueen</option> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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47 </param> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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48 </inputs> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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49 |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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50 <outputs> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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51 <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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52 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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53 <data name="scores_out" label="${tool.name}_${dataMatrix_in.name}.kmeans" format="tabular" ></data> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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54 </outputs> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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55 |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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56 <tests> |
1
02cafb660b72
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit f600ce8a783df16e49272341dce0fc6bbc299b0a
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57 <test> |
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6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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58 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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59 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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60 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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61 <param name="ksamples" value="3,4"/> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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62 <param name="kfeatures" value="5,6,7"/> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
eschen42
parents:
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63 <param name="iter_max" value="10"/> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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64 <param name="nstart" value="1"/> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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65 <param name="algorithm" value="Hartigan-Wong"/> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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66 <output name="scores_out"> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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67 <assert_contents> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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68 <has_text text="proportion" /> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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69 <has_text text="0.87482" /> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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70 <has_text text="0.89248" /> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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71 <has_text text="0.95355" /> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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72 <has_text text="0.95673" /> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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73 <has_text text="0.95963" /> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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74 </assert_contents> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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75 </output> |
6ccbe18131a6
planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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76 </test> |
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77 </tests> |
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78 |
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79 <help> |
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80 <![CDATA[ |
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81 |
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82 **Author** - Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu) |
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83 |
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84 --------------------------------------------------------------------------- |
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85 |
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86 |
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87 **Source** - The source code for the w4mkmeans tool is available (from the Hegeman lab github repository) at https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper |
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88 |
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89 **R code used** - The R code invoked by this wrapper is the R 'stats::kmeans' package |
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90 |
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91 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
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92 |
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93 |
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94 **Tool updates** |
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95 |
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96 See the **NEWS** section at the bottom of this page |
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97 |
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98 --------------------------------------------------- |
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99 |
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100 =========================== |
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101 K-means for W4M data matrix |
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102 =========================== |
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103 |
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104 ----------- |
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105 Description |
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106 ----------- |
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107 |
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108 Calculate K-means for sample-clusters (or feature-clusters, or both) using W4M dataMatrix (i.e., XCMS-preprocessed data files) as input. |
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109 |
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110 *Please note that XCMS refers to features as 'variables'. This documentation does not use either term consistently.* |
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111 |
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112 |
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113 ----------------- |
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114 Workflow Position |
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115 ----------------- |
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116 |
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117 - Tool category: Statistical Analysis |
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118 - Upstream tool category: Preprocessing |
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119 - Downstream tool categories: Statistical Analysis |
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120 |
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121 |
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122 ---------- |
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123 Motivation |
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124 ---------- |
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125 |
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126 This tool clusters samples, features (variables), or both from the W4M dataMatrix and writes the results to new columns in sampleMetadata, variableMetadata, or both, respectively. |
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127 |
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128 - If several, comma-separated K's are supplied, then one column is added for each K. |
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129 - This clustering is **not** hierarchical; each member of a cluster is not a member of any other cluster. |
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130 - For feature-clustering, each feature is assigned to a cluster such that the feature's response for all samples is closer to the mean of all features for that cluster than to the mean for any other cluster. |
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131 - For sample-clustering, each sample is assigned to a cluster such that the sample's response for all features is closer to the mean of all samples for that cluster than to the mean for any other cluster. |
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132 |
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133 |
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134 ----------- |
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135 Input files |
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136 ----------- |
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137 |
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138 +--------------------------------------------+------------+ |
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139 | File | Format | |
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140 +============================================+============+ |
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141 | Data matrix | tabular | |
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142 +--------------------------------------------+------------+ |
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143 | Sample metadata | tabular | |
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144 +--------------------------------------------+------------+ |
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145 | Variable (i.e., feature) metadata | tabular | |
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146 +--------------------------------------------+------------+ |
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147 |
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148 |
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149 ---------- |
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150 Parameters |
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151 ---------- |
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152 |
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153 **Data matrix** - input-file dataset |
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154 |
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155 - XCMS variable x sample 'dataMatrix' (tabular separated values) file of the numeric data matrix, with . as decimal, and NA for missing values; the table must not contain metadata apart from row and column names; the row and column names must be identical to the rownames of the sample and feature metadata, respectively (see below) |
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156 |
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157 **Sample metadata** - input-file dataset |
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158 |
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159 - XCMS sample x metadata 'sampleMetadata' (tabular separated values) file of the numeric and/or character sample metadata, with . as decimal and NA for missing values |
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160 |
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161 **Feature metadata** - input-file dataset |
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162 |
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163 - XCMS variable x metadata 'variableMetadata' (tabular separated values) file of the numeric and/or character feature metadata, with . as decimal and NA for missing values |
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164 |
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165 **kfeatures** - K or K's for features (default = 0) |
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166 |
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167 - integer or comma-separated integers ; zero (the default) or less will result in no calculation. |
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168 |
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169 **ksamples** - K or K-range for samples (default = 0) |
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170 |
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171 - integer or comma-separated integers ; zero (the default) or less will result in no calculation. |
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172 |
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173 **iter_max** - maximum_iterations (default = 10) |
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174 |
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175 - maximum number of iterations per calculation (see https://stat.ethz.ch/R-manual/R-devel/library/stats/html/kmeans.html). |
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176 |
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177 **nstart** - how many random sets should be chosen (default = 1) |
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178 |
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179 - maximum number of iterations per calculation (see https://stat.ethz.ch/R-manual/R-devel/library/stats/html/kmeans.html). |
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180 |
1
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181 **categorical_prefix** - character(s) to add as prefix to category number (default = 'k') |
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182 |
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183 - some tools treat only non-numeric data as categorical; this prefix ('k' by default) ensures that clusters data will be treated as categorical; an empty string is permitted here if desired (and succeeding tools accept integers as categorical data). |
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184 |
0
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185 ------------ |
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186 Output files |
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187 ------------ |
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188 |
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189 **XCMS sampleMetadata** - (tabular separated values) file identical to the Sample metadata file given as an input argument, excepting one column added for each K |
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190 |
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191 - **k#** - cluster number for clustering samples with K = # |
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192 |
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193 **XCMS variableMetadata** - (tabular separated values) file identical to the Feature metadata file given as an input argument, excepting one column added for each K |
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194 |
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195 - **k#** - cluster number for clustering features with K = # |
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196 |
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197 **scores** - (tabular separated values) file with one line for each K. |
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198 |
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199 - **clusterOn** - what was clustered - either 'sample' or 'feature' |
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200 - **k** - the chosen K for clustering |
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201 - **totalSS** - total (*between-treatements* plus total of *within-treatements*) sum of squares |
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202 - **betweenSS** - *between-treatements* sum of squares |
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203 - **proportion** - betweenSS / totalSS |
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204 |
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205 --------------- |
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206 Working example |
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207 --------------- |
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208 |
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209 **Input files** |
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210 |
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211 +-------------------+-------------------------------------------------------------------------------------------------------------------+ |
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212 | Input File | Download from URL | |
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213 +===================+===================================================================================================================+ |
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214 | Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mkmeans_galaxy_wrapper/master/test-data/input_dataMatrix.tsv | |
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215 +-------------------+-------------------------------------------------------------------------------------------------------------------+ |
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216 | Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mkmeans_galaxy_wrapper/master/test-data/input_sampleMetadata.tsv | |
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217 +-------------------+-------------------------------------------------------------------------------------------------------------------+ |
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218 | Feature metadata | https://raw.githubusercontent.com/HegemanLab/w4mkmeans_galaxy_wrapper/master/test-data/input_variableMetadata.tsv | |
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219 +-------------------+-------------------------------------------------------------------------------------------------------------------+ |
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220 |
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221 **Other input parameters** |
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222 |
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223 +-----------------+---------------+ |
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224 | Input Parameter | Value | |
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225 +=================+===============+ |
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226 | ksamples | 3,4 | |
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227 +-----------------+---------------+ |
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228 | kfeatures | 5,6,7 | |
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229 +-----------------+---------------+ |
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230 | iter_max | 10 | |
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231 +-----------------+---------------+ |
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232 | nstart | 1 | |
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233 +-----------------+---------------+ |
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234 | algorithm | Hartigan-Wong | |
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235 +-----------------+---------------+ |
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236 |
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237 ---- |
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238 NEWS |
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239 ---- |
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240 |
1
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241 - August 2017, Version 0.98.3 - Add (optional) prefix to category numbers for downstream tools that treat only non-numeric data as categorical. |
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242 - August 2017, Version 0.98.1 - First release |
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243 |
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244 --------- |
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245 Citations |
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246 --------- |
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247 |
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248 ]]> |
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249 </help> |
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250 <citations> |
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251 <citation type="bibtex"><![CDATA[ |
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252 @incollection{RCoreTeam2017, |
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253 title = {stats::kmeans - K-Means Clustering}, |
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254 booktitle = {R: A Language and Environment for Statistical Computing}, |
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255 author = {{R Core Team}}, |
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256 publisher = {R Foundation for Statistical Computing}, |
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257 address = {Vienna, Austria}, |
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258 year = {2017}, |
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259 url = {https://stat.ethz.ch/R-manual/R-devel/library/stats/html/kmeans.html}, |
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260 } |
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261 ]]></citation> |
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262 <!-- Forgy algorithm --> |
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263 <citation type="bibtex"><![CDATA[ |
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264 @article{forgy65, |
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265 added-at = {2006-03-23T12:22:43.000+0100}, |
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266 author = {Forgy, E.}, |
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267 biburl = {https://www.bibsonomy.org/bibtex/21e31409932ce91df646c4731350e1207/hotho}, |
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268 interhash = {c86383cba8cfe00d5e6ef200016aca3f}, |
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269 intrahash = {1e31409932ce91df646c4731350e1207}, |
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270 journal = {Biometrics}, |
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271 keywords = {clustering kmeans}, |
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272 number = 3, |
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273 pages = {768-769}, |
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274 timestamp = {2006-03-23T12:22:43.000+0100}, |
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275 title = {Cluster Analysis of Multivariate Data: Efficiency versus Interpretability of Classification}, |
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276 volume = 21, |
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277 year = 1965 |
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278 } |
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279 ]]></citation> |
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280 <!-- W4M 3.0 - Guitton et al. 2017--> |
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281 <citation type="doi">10.1016/j.biocel.2017.07.002</citation> |
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282 <!-- W4M 2.5 - Giacomini et al. 2014 --> |
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283 <citation type="doi">10.1093/bioinformatics/btu813</citation> |
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284 <!-- Hartigan and Wong algorithm --> |
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285 <citation type="bibtex"><![CDATA[ |
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286 @article{Hartigan79, |
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287 added-at = {2007-02-27T16:22:09.000+0100}, |
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288 author = {Hartigan, J. and Wong, M.}, |
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289 biburl = {https://www.bibsonomy.org/bibtex/23d8bfc440c5725783876929c022f67ce/pierpaolo.pk81}, |
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290 description = {WSD}, |
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291 interhash = {10d6d33920d9af578a4d0a556dc1477d}, |
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292 intrahash = {3d8bfc440c5725783876929c022f67ce}, |
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293 journal = {Applied Statistics}, |
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294 keywords = {imported}, |
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295 pages = {100-108}, |
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296 timestamp = {2007-02-27T16:22:11.000+0100}, |
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297 title = {Algorithm AS136: A k-means clustering algorithm}, |
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298 volume = 28, |
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299 year = 1979 |
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300 } |
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301 ]]></citation> |
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302 <!-- Lloyd algorithm --> |
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303 <citation type="doi">10.1109/TIT.1982.1056489</citation> |
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304 <!-- MacQueen algorithm --> |
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305 <citation type="bibtex"><![CDATA[ |
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306 @inproceedings{MacQueen1967, |
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307 added-at = {2011-01-11T13:35:01.000+0100}, |
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308 author = {MacQueen, J. B.}, |
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309 biburl = {https://www.bibsonomy.org/bibtex/25dcdb8cd9fba78e0e791af619d61d66d/enitsirhc}, |
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310 booktitle = {Proc. of the fifth Berkeley Symposium on Mathematical Statistics and Probability}, |
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311 editor = {Cam, L. M. Le and Neyman, J.}, |
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312 interhash = {8d7d4dfe7d3a06b8c9c3c2bb7aa91e28}, |
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313 intrahash = {5dcdb8cd9fba78e0e791af619d61d66d}, |
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314 keywords = {kmeans clustering}, |
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315 pages = {281-297}, |
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316 publisher = {University of California Press}, |
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317 timestamp = {2011-01-11T13:35:01.000+0100}, |
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318 title = {Some Methods for Classification and Analysis of MultiVariate Observations}, |
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319 volume = 1, |
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320 year = 1967 |
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321 } |
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322 ]]></citation> |
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323 </citations> |
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planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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324 <!-- |
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planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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325 vim:et:sw=2:ts=2: |
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planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 299e5c7fdb0d6eb0773f3660009f6d63c2082a8d
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326 --> </tool> |