Mercurial > repos > ebi-gxa > sc3_kmeans

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
author ebi-gxa
date Wed, 03 Apr 2019 11:27:08 -0400
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b3c3cf813a49 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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1 <?xml version="1.0" encoding="utf-8"?>
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2 <tool id="sc3_kmeans" name="SC3 K-Means" version="@TOOL_VERSION@+galaxy0">
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3 <description>perform k-means clustering</description>
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4 <macros>
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5 <import>sc3-macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 sc3-sc3-kmeans.R -i '${sc3_transformed}'
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10 #if $choose.method == "file":
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11 -k '${choose.sc3_estimated_k}'
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12 #else
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13 -k '${choose.input_k}'
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14 #end if
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15 -o '${sc3_kmeans}'
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16 ]]></command>
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17
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18 <inputs>
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19 <param name="sc3_transformed" type="data" format="rdata" label="Serialised sc3 SingleCellExperiment object with transformed distances"/>
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21 <conditional name="choose">
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22 <param name="method" type="select" label="Method to supply K">
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23 <option value="input">Enter K as an integer</option>
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24 <option value="file">Provide a text file containing K</option>
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25 </param>
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26 <when value="input">
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27 <param name="input_k" type="integer" value="0" label="Integer K as the number of clusters for kmeans"/>
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28 </when>
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29 <when value="file">
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30 <param name="sc3_estimated_k" type="data" format="txt" label="Text file containing estimated K"/>
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31 </when>
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32 </conditional>
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33 </inputs>
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34
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35 <outputs>
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36 <data name="sc3_kmeans" format="rdata" label="${tool.name} on ${on_string}: serialised sc3 SingleCellExperiment object storing the k-means clusters"/>
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37 </outputs>
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38
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39 <tests>
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40 <test>
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41 <param name="sc3_transformed" value="sc3_transformed.rds"/>
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42 <param name="sc3_estimated_k" value="K_size"/>
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43 <output name="sc3_kmeans" file="sc3_kmeans.rds"/>
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44 </test>
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45 </tests>
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46
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47 <help><![CDATA[
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48 =========================================
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49 This function performs kmeans clustering.
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50 =========================================
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51
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52 It uses transformed distance matrix contained in the transformations item of the
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53 sc3 slot of the metadata(object). It then creates and populates the following
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54 items of the sc3 slot:
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55
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56 - kmeans: contains a list of kmeans clusterings.
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57
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58 @HELP@
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59
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60 @VERSION_HISTORY@
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61 ]]></help>
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62 <expand macro="citations" />
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63 </tool>