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comparison w4mkmeans.xml @ 1:02cafb660b72 draft

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planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit f600ce8a783df16e49272341dce0fc6bbc299b0a
author eschen42
date Wed, 09 Aug 2017 18:06:55 -0400
parents 6ccbe18131a6
children c415b7dc6f37
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0:6ccbe18131a6 1:02cafb660b72
1 <tool id="w4mkmeans" name="Kmeans_for_W4M" version="0.98.1"> 1 <tool id="w4mkmeans" name="w4mKmeans" version="0.98.3">
2 <description>Calculate K-means for dataMatrix features or samples</description> 2 <description>Calculate K-means for W4M dataMatrix features or samples</description>
3 3
4 <requirements> 4 <requirements>
5 <requirement type="package" version="3.3.2">r-base</requirement> 5 <requirement type="package" version="3.3.2">r-base</requirement>
6 <requirement type="package" version="1.1_4">r-batch</requirement> 6 <requirement type="package" version="1.1_4">r-batch</requirement>
7 </requirements> 7 </requirements>
12 12
13 13
14 <command detect_errors="aggressive"><![CDATA[ 14 <command detect_errors="aggressive"><![CDATA[
15 Rscript $__tool_directory__/w4mkmeans_wrapper.R 15 Rscript $__tool_directory__/w4mkmeans_wrapper.R
16 tool_directory $__tool_directory__ 16 tool_directory $__tool_directory__
17 algorithm '$algorithm'
18 categorical_prefix '$categoricalPrefix'
17 data_matrix_path '$dataMatrix_in' 19 data_matrix_path '$dataMatrix_in'
20 iter_max '$iter_max'
21 kfeatures '$kfeatures'
22 ksamples '$ksamples'
23 nstart '$nstart'
24 sampleMetadata_out '$sampleMetadata_out'
25 sample_metadata_path '$sampleMetadata_in'
26 scores_out '$scores_out'
27 slots "\${GALAXY_SLOTS:-1}"
28 variableMetadata_out '$variableMetadata_out'
18 variable_metadata_path '$variableMetadata_in' 29 variable_metadata_path '$variableMetadata_in'
19 sample_metadata_path '$sampleMetadata_in'
20 ksamples '$ksamples'
21 kfeatures '$kfeatures'
22 iter_max '$iter_max'
23 nstart '$nstart'
24 algorithm '$algorithm'
25 scores_out '$scores_out'
26 sampleMetadata_out '$sampleMetadata_out'
27 variableMetadata_out '$variableMetadata_out'
28 slots "\${GALAXY_SLOTS:-1}"
29 ; echo exit code $? 30 ; echo exit code $?
30 ]]></command> 31 ]]></command>
31 32
32 <inputs> 33 <inputs>
33 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, separator: tab" /> 34 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, separator: tab" />
34 <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata columns, separator: tab" /> 35 <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata columns, separator: tab" />
35 <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata columns, separator: tab" /> 36 <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata columns, separator: tab" />
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'." />
36 <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." /> 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." />
37 <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." /> 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." />
38 <param name="iter_max" label="Max number of iterations" type="text" value = "10" help="[iter_max] The maximum number of iterations allowed; default 10." /> 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." />
39 <param name="nstart" label="Number of random sets" type="text" value = "1" help="[nstart] How many random sets should be chosen; default 1." /> 41 <param name="nstart" label="Number of random sets" type="text" value = "1" help="[nstart] How many random sets should be chosen; default 1." />
40 <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 references for further info."> 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.">
41 <option value="Forgy">Forgy</option> 43 <option value="Forgy">Forgy</option>
42 <option value="Hartigan-Wong" selected="True">Hartigan-Wong</option> 44 <option value="Hartigan-Wong" selected="True">Hartigan-Wong</option>
43 <option value="Lloyd">Lloyd</option> 45 <option value="Lloyd">Lloyd</option>
44 <option value="MacQueen">MacQueen</option> 46 <option value="MacQueen">MacQueen</option>
45 </param> 47 </param>
50 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data> 52 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>
51 <data name="scores_out" label="${tool.name}_${dataMatrix_in.name}.kmeans" format="tabular" ></data> 53 <data name="scores_out" label="${tool.name}_${dataMatrix_in.name}.kmeans" format="tabular" ></data>
52 </outputs> 54 </outputs>
53 55
54 <tests> 56 <tests>
55 <test> 57 <test>
56 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/> 58 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
57 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/> 59 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
58 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/> 60 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
59 <param name="ksamples" value="3,4"/> 61 <param name="ksamples" value="3,4"/>
60 <param name="kfeatures" value="5,6,7"/> 62 <param name="kfeatures" value="5,6,7"/>
174 176
175 **nstart** - how many random sets should be chosen (default = 1) 177 **nstart** - how many random sets should be chosen (default = 1)
176 178
177 - maximum number of iterations per calculation (see https://stat.ethz.ch/R-manual/R-devel/library/stats/html/kmeans.html). 179 - maximum number of iterations per calculation (see https://stat.ethz.ch/R-manual/R-devel/library/stats/html/kmeans.html).
178 180
181 **categorical_prefix** - character(s) to add as prefix to category number (default = 'k')
182
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).
184
179 ------------ 185 ------------
180 Output files 186 Output files
181 ------------ 187 ------------
182 188
183 **XCMS sampleMetadata** - (tabular separated values) file identical to the Sample metadata file given as an input argument, excepting one column added for each K 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
230 236
231 ---- 237 ----
232 NEWS 238 NEWS
233 ---- 239 ----
234 240
235 August 2017, Version 0.98.1 - First release 241 - August 2017, Version 0.98.3 - Add (optional) prefix to category numbers for downstream tools that treat only non-numeric data as categorical.
242 - August 2017, Version 0.98.1 - First release
236 243
237 --------- 244 ---------
238 Citations 245 Citations
239 --------- 246 ---------
240 247