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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 11:25:01 -0400
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1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="sc3_estimate_k" name="SC3 Estimate" version="@TOOL_VERSION@+galaxy0">
3 <description>the number of clusters for 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-estimate-k.R -i '${sc3_prepared}' -t '${sc3_estimated_k}' -o sc3_estimated.rds &&
10
11 echo -n "estimated k = " && cat ${sc3_estimated_k}
12 ]]></command>
13
14 <inputs>
15 <param type="data" name="sc3_prepared" format="rdata" label="Serialised sc3 SingleCellExperiment object"/>
16 </inputs>
17
18 <outputs>
19 <data name="sc3_estimated_k" format="txt" label="${tool.name} on ${on_string}: txt file containting estimated K value"/>
20 </outputs>
21
22 <tests>
23 <test>
24 <param name="sc3_prepared" value="sc3_prepared.rds"/>
25 <output name="sc3_estimated_k" file="sc3-estimated-k.txt"/>
26 </test>
27 </tests>
28
29 <help><![CDATA[
30 ========================================================================================
31 Uses Tracy-Widom theory on random matrices to estimate the optimal number of clusters k.
32 ========================================================================================
33
34 It creates and populates the k_estimation item of the sc3 slot of the metadata(object).
35
36 @HELP@
37
38 @VERSION_HISTORY@
39 ]]></help>
40 <expand macro="citations" />
41 </tool>