Mercurial > repos > ebi-gxa > sc3_kmeans
comparison sc3-kmeans.xml @ 0:b3c3cf813a49 draft default tip
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
author | ebi-gxa |
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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> |