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comparison mixomics_plotindiv.xml @ 0:d0b77b926863 draft

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"
author ppericard
date Tue, 23 Jun 2020 19:57:35 -0400
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1 <tool id="mixomics_plotindiv" name="mixOmics plotIndiv" version="1.0" profile="16.04" workflow_compatible="true">
2
3 <description>provides scatter plots for individuals (experimental units) representation in (sparse)(I)PCA,(regularized)CCA, (sparse)PLS(DA) and (sparse)(R)GCCA(DA)</description>
4
5 <requirements>
6 <requirement type="package" version="6.12">bioconductor-mixomics</requirement>
7 <requirement type="package" version="2.0">r-argparse</requirement>
8 </requirements>
9
10 <stdio>
11 <!-- <exit_code range="1:" level="fatal" /> -->
12 </stdio>
13
14 <command detect_errors="aggressive">
15 <![CDATA[
16 Rscript
17 ${__tool_directory__}/mixomics_plotindiv_script.R
18 --input_rdata $input_rdata
19 $adv.legend
20 $adv.ellipse
21 --output_pdf $output_pdf
22 ]]>
23 </command>
24
25 <inputs>
26 <param name="input_rdata" type="data" format="rdata"
27 label="Input RData file from (sparse)(I)PCA, (regularized)CCA, (sparse)PLS(DA) or (sparse)(R)GCCA(DA)"
28 help="This is the RData output file from the block.splsda function." />
29 <section name="adv" title="Advanced Options" expanded="false">
30 <param name="legend" type="boolean" checked="true" truevalue="--legend" falsevalue=""
31 label="Plot legend" />
32 <param name="ellipse" type="boolean" checked="true" truevalue="--ellipse" falsevalue=""
33 label="Plot ellipse plots" />
34 </section>
35 </inputs>
36
37 <outputs>
38 <data name="output_pdf" format="pdf" label="plotIndiv.pdf" />
39 </outputs>
40
41 <tests>
42 <test>
43 <param name="input_rdata" value="out_rdata.rdata" />
44 <output name="output_pdf" value="out_plotIndiv.pdf" />
45 </test>
46 </tests>
47
48 <help>
49 <![CDATA[
50 .. class:: infomark
51
52 **Authors** Pierre Pericard (pierre.pericard@pasteur-lille.fr)
53
54 ---------------------------------------------------
55
56 .. class:: infomark
57
58 **Please cite**
59
60 Rohart F, Gautier B, Singh A, Lê Cao KA (2017) mixOmics: An R package for ‘omics feature selection and multiple data integration.
61 PLOS Computational Biology 13(11): e1005752. https://doi.org/10.1371/journal.pcbi.1005752
62
63 ---------------------------------------------------
64
65 ==================
66 mixOmics plotIndiv
67 ==================
68
69 -----------
70 Description
71 -----------
72
73 The plotIndiv function is part of the mixOmics package for exploration and integration of Omics datasets.
74 Provides scatter plots for individuals (experimental units) representation in (sparse)(I)PCA,(regularized)CCA, (sparse)PLS(DA) and (sparse)(R)GCCA(DA).
75
76 -----------
77 Input files
78 -----------
79
80 +-------------------------------+------------+
81 | Parameter : num + label | Format |
82 +===============================+============+
83 | 1 : Rdata block.splsda output | Rdata |
84 +-------------------------------+------------+
85
86 ----------
87 Parameters
88 ----------
89
90 Advanced options:
91 =================
92
93 Plot legend
94
95 Plot ellipse plots
96
97 ------------
98 Output files
99 ------------
100
101 plotIndiv.pdf
102 A pdf file with scatter plots for individuals
103
104 ]]>
105 </help>
106
107 <citations>
108 <citation type="doi">10.1371/journal.pcbi.1005752</citation>
109 </citations>
110
111 </tool>