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comparison mixomics_plotvar.xml @ 0:bea08702ed51 draft

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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
author ppericard
date Fri, 17 May 2019 05:00:22 -0400
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1 <tool id="mixomics_plotvar" name="mixOmics plotVar" version="0.1.0" profile="16.04" workflow_compatible="true">
2
3 <description>provides variables representation for (regularized) CCA, (sparse) PLS regression, PCA and (sparse) Regularized generalised CCA</description>
4
5 <requirements>
6 <requirement type="package" version="6.8">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_plotvar_script.R
18 --input_rdata $input_rdata
19 $adv.legend
20 --cutoff $adv.cutoff
21 --output_pdf $output_pdf
22 ]]>
23 </command>
24
25 <inputs>
26 <param name="input_rdata" type="data" format="rdata" label="Input RData file from (sparse)(I)PCA, (regularized)CCA, (sparse)PLS(DA) or (sparse)(R)GCCA(DA)"/>
27 <section name="adv" title="Advanced Options" expanded="false">
28 <param name="legend" type="boolean" checked="true" truevalue="--legend" falsevalue="" label="Plot legend"/>
29 <param name="cutoff" type="float" value="0.85" min="0" max="1" label="Cut-off" />
30 </section>
31 </inputs>
32
33 <outputs>
34 <data name="output_pdf" format="pdf" label="plotVar.pdf" />
35 </outputs>
36
37 <tests>
38 <test>
39 <param name="input_rdata" value="out_rdata.rdata" />
40 <output name="output_pdf" value="out_plotVar.pdf" />
41 </test>
42 </tests>
43
44 <help>
45 <![CDATA[
46 .. class:: infomark
47
48 **Authors** Pierre Pericard (pierre.pericard@pasteur-lille.fr)
49
50 ---------------------------------------------------
51
52 .. class:: infomark
53
54 **Please cite**
55
56 Rohart F, Gautier B, Singh A, Lê Cao KA (2017) mixOmics: An R package for ‘omics feature selection and multiple data integration.
57 PLOS Computational Biology 13(11): e1005752. https://doi.org/10.1371/journal.pcbi.1005752
58
59 ---------------------------------------------------
60
61 ================
62 mixOmics plotVar
63 ================
64
65 -----------
66 Description
67 -----------
68
69 The plotVar function is part of the mixOmics package for exploration and integration of Omics datasets.
70 Provides variables representation for (regularized) CCA, (sparse) PLS regression, PCA and (sparse) Regularized generalised CCA.
71
72 -----------
73 Input files
74 -----------
75
76 +-------------------------------+------------+
77 | Parameter : num + label | Format |
78 +===============================+============+
79 | 1 : Rdata block.splsda output | Rdata |
80 +-------------------------------+------------+
81
82 ----------
83 Parameters
84 ----------
85
86 Advanced options:
87 =================
88
89 Plot legend
90
91 Cut-off
92
93 ------------
94 Output files
95 ------------
96
97 plotIndiv.pdf
98 A pdf file with scatter plots for individuals
99
100 ]]>
101 </help>
102
103 <citations>
104 <citation type="doi">10.1371/journal.pcbi.1005752</citation>
105 </citations>
106
107 </tool>