comparison sc3-calc-biology.xml @ 0:2ee3dd245f72 draft default tip

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 11:32:26 -0400
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1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="sc3_calc_biology" name="SC3 DiffExp" version="@TOOL_VERSION@+galaxy1">
3 <description>calculates DE genes, marker genes and cell outliers</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-calc-biology.R -i '${sc3_consensus}' -o '${sc3_biology_markers}' -t '${sc3_biology_markers_tsv}' -k '${ks}' -r '${regime}'
10 ]]></command>
11
12 <inputs>
13 <param name="sc3_consensus" type="data" format="rdata" label="Serialised sc3 SingleCellExperiment object with stored consensus kmeans clustering"/>
14
15 <param name="ks" argument="--ks" type="text" label="An integer or comma-separated list of integers">
16 <validator type="regex" message="Please only enter integers or comma-separated list of integers">^[0-9]+(,[0-9]+)*$</validator>
17 </param>
18
19 <param name="regime" argument="--regime" type="select" label="Biological analysis to perform">
20 <option value="marker" selected="true">Marker gene identification</option>
21 <option value="de">Differential expression</option>
22 <option value="outl">Outlier identification</option>
23 </param>
24 </inputs>
25
26 <outputs>
27 <data name="sc3_biology_markers" format="rdata" label="${tool.name} on ${on_string}: serialised sc3 SingleCellExperiment storing the DE markers"/>
28 <data name="sc3_biology_markers_tsv" format="tsv" label="${tool.name} on ${on_string}: tsv table storing the DE markers"/>
29 </outputs>
30
31 <tests>
32 <test>
33 <param name="sc3_consensus" value="sc3_consensus.rds"/>
34 <param name="ks" value="7,8"/>
35 <param name="regime" value="marker"/>
36 <output name="sc3_biology_markers" file="sc3_bio_sce.rds"/>
37 <output name="sc3_biology_markers_tsv" file="sc3_biology_markers.tsv"/>
38 </test>
39 </tests>
40
41 <help><![CDATA[
42 ========================================================
43 This function performs differential expression analysis.
44 ========================================================
45
46 Calculate differentially expressed (DE) genes, marker genes and cell outliers
47 based on the consensus SC3 clusterings.
48
49 @HELP@
50
51 @VERSION_HISTORY@
52 ]]></help>
53 <expand macro="citations" />
54 </tool>