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comparison mixomics_plotvar.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_plotvar" name="mixOmics plotVar" version="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="6.12">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_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"
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="cutoff" type="float" value="0" min="0" max="1"
33 label="Cut-off"
34 help="Only selected variables whose correlation with the first or second axis is greater than Cut-off in absolute value will be plotted." />
35 </section>
36 </inputs>
37
38 <outputs>
39 <data name="output_pdf" format="pdf" label="plotVar.pdf" />
40 </outputs>
41
42 <tests>
43 <test>
44 <param name="input_rdata" value="out_rdata.rdata" />
45 <output name="output_pdf" value="out_plotVar.pdf" />
46 </test>
47 </tests>
48
49 <help>
50 <![CDATA[
51 .. class:: infomark
52
53 **Authors** Pierre Pericard (pierre.pericard@pasteur-lille.fr)
54
55 ---------------------------------------------------
56
57 .. class:: infomark
58
59 **Please cite**
60
61 Rohart F, Gautier B, Singh A, Lê Cao KA (2017) mixOmics: An R package for ‘omics feature selection and multiple data integration.
62 PLOS Computational Biology 13(11): e1005752. https://doi.org/10.1371/journal.pcbi.1005752
63
64 ---------------------------------------------------
65
66 ================
67 mixOmics plotVar
68 ================
69
70 -----------
71 Description
72 -----------
73
74 The plotVar function is part of the mixOmics package for exploration and integration of Omics datasets.
75 Provides variables representation for (regularized) CCA, (sparse) PLS regression, PCA and (sparse) Regularized generalised CCA.
76
77 -----------
78 Input files
79 -----------
80
81 +-------------------------------+------------+
82 | Parameter : num + label | Format |
83 +===============================+============+
84 | 1 : Rdata block.splsda output | Rdata |
85 +-------------------------------+------------+
86
87 ----------
88 Parameters
89 ----------
90
91 Advanced options:
92 =================
93
94 Plot legend
95
96 Cut-off
97
98 ------------
99 Output files
100 ------------
101
102 plotIndiv.pdf
103 A pdf file with scatter plots for individuals
104
105 ]]>
106 </help>
107
108 <citations>
109 <citation type="doi">10.1371/journal.pcbi.1005752</citation>
110 </citations>
111
112 </tool>