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comparison sc3-kmeans.xml @ 0:b3c3cf813a49 draft default tip

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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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1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="sc3_kmeans" name="SC3 K-Means" version="@TOOL_VERSION@+galaxy0">
3 <description>perform k-means clustering</description>
4 <macros>
5 <import>sc3-macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[
9 sc3-sc3-kmeans.R -i '${sc3_transformed}'
10 #if $choose.method == "file":
11 -k '${choose.sc3_estimated_k}'
12 #else
13 -k '${choose.input_k}'
14 #end if
15 -o '${sc3_kmeans}'
16 ]]></command>
17
18 <inputs>
19 <param name="sc3_transformed" type="data" format="rdata" label="Serialised sc3 SingleCellExperiment object with transformed distances"/>
20
21 <conditional name="choose">
22 <param name="method" type="select" label="Method to supply K">
23 <option value="input">Enter K as an integer</option>
24 <option value="file">Provide a text file containing K</option>
25 </param>
26 <when value="input">
27 <param name="input_k" type="integer" value="0" label="Integer K as the number of clusters for kmeans"/>
28 </when>
29 <when value="file">
30 <param name="sc3_estimated_k" type="data" format="txt" label="Text file containing estimated K"/>
31 </when>
32 </conditional>
33 </inputs>
34
35 <outputs>
36 <data name="sc3_kmeans" format="rdata" label="${tool.name} on ${on_string}: serialised sc3 SingleCellExperiment object storing the k-means clusters"/>
37 </outputs>
38
39 <tests>
40 <test>
41 <param name="sc3_transformed" value="sc3_transformed.rds"/>
42 <param name="sc3_estimated_k" value="K_size"/>
43 <output name="sc3_kmeans" file="sc3_kmeans.rds"/>
44 </test>
45 </tests>
46
47 <help><![CDATA[
48 =========================================
49 This function performs kmeans clustering.
50 =========================================
51
52 It uses transformed distance matrix contained in the transformations item of the
53 sc3 slot of the metadata(object). It then creates and populates the following
54 items of the sc3 slot:
55
56 - kmeans: contains a list of kmeans clusterings.
57
58 @HELP@
59
60 @VERSION_HISTORY@
61 ]]></help>
62 <expand macro="citations" />
63 </tool>