Mercurial > repos > ppericard > mixomics_blocksplsda

annotate mixomics_plotindiv.xml @ 6:bc28839b17fb draft default tip

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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit f2b28f1a77491a26f8ac753b3623400d8485470a
author ppericard
date Tue, 10 Mar 2020 06:51:08 -0400
parents b0ab97ffc2a1
children
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1 <tool id="mixomics_plotindiv" name="mixOmics plotIndiv" version="0.3.0" profile="16.04" workflow_compatible="true">
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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>
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5 <requirements>
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6 <requirement type="package" version="6.8">bioconductor-mixomics</requirement>
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7 <requirement type="package" version="2.0">r-argparse</requirement>
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8 </requirements>
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9
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10 <stdio>
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11 <!-- <exit_code range="1:" level="fatal" /> -->
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12 </stdio>
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14 <command detect_errors="aggressive">
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15 <![CDATA[
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16 Rscript
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17 ${__tool_directory__}/mixomics_plotindiv_script.R
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18 --input_rdata $input_rdata
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19 $adv.legend
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20 $adv.ellipse
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21 --output_pdf $output_pdf
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22 ]]>
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23 </command>
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25 <inputs>
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26 <param name="input_rdata" type="data" format="rdata"
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27 label="Input RData file from (sparse)(I)PCA, (regularized)CCA, (sparse)PLS(DA) or (sparse)(R)GCCA(DA)"
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28 help="This is the RData output file from the block.splsda function." />
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29 <section name="adv" title="Advanced Options" expanded="false">
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30 <param name="legend" type="boolean" checked="true" truevalue="--legend" falsevalue=""
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31 label="Plot legend" />
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32 <param name="ellipse" type="boolean" checked="true" truevalue="--ellipse" falsevalue=""
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33 label="Plot ellipse plots" />
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34 </section>
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35 </inputs>
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37 <outputs>
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38 <data name="output_pdf" format="pdf" label="plotIndiv.pdf" />
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39 </outputs>
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41 <tests>
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42 <test>
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43 <param name="input_rdata" value="out_rdata.rdata" />
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44 <output name="output_pdf" value="out_plotIndiv.pdf" />
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45 </test>
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46 </tests>
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48 <help>
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49 <![CDATA[
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50 .. class:: infomark
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51
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52 **Authors** Pierre Pericard (pierre.pericard@pasteur-lille.fr)
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54 ---------------------------------------------------
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55
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56 .. class:: infomark
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57
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58 **Please cite**
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59
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60 Rohart F, Gautier B, Singh A, Lê Cao KA (2017) mixOmics: An R package for ‘omics feature selection and multiple data integration.
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61 PLOS Computational Biology 13(11): e1005752. https://doi.org/10.1371/journal.pcbi.1005752
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62
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63 ---------------------------------------------------
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64
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65 ==================
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66 mixOmics plotIndiv
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67 ==================
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68
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69 -----------
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70 Description
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71 -----------
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72
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73 The plotIndiv function is part of the mixOmics package for exploration and integration of Omics datasets.
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74 Provides scatter plots for individuals (experimental units) representation in (sparse)(I)PCA,(regularized)CCA, (sparse)PLS(DA) and (sparse)(R)GCCA(DA).
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75
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76 -----------
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77 Input files
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78 -----------
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79
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80 +-------------------------------+------------+
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81 | Parameter : num + label | Format |
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82 +===============================+============+
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83 | 1 : Rdata block.splsda output | Rdata |
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84 +-------------------------------+------------+
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85
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86 ----------
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87 Parameters
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88 ----------
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89
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90 Advanced options:
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91 =================
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92
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93 Plot legend
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94
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95 Plot ellipse plots
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96
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97 ------------
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98 Output files
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99 ------------
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101 plotIndiv.pdf
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102 A pdf file with scatter plots for individuals
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103
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104 ]]>
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105 </help>
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106
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107 <citations>
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108 <citation type="doi">10.1371/journal.pcbi.1005752</citation>
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109 </citations>
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110
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111 </tool>