Mercurial > repos > eschen42 > w4mkmeans
comparison 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 |
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0:6ccbe18131a6 | 1:02cafb660b72 |
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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 |