Mercurial > repos > ppericard > mixomics_blocksplsda

annotate mixomics_plotvar.xml @ 5:1ee8d2c20c0a draft

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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 25773bd7a90072f9782df823969b282e4fe29252
author ppericard
date Tue, 10 Mar 2020 06:27:02 -0400
parents b0ab97ffc2a1
children
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1 <tool id="mixomics_plotvar" name="mixOmics plotVar" version="0.3.0" profile="16.04" workflow_compatible="true">
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3 <description>provides variables representation for (regularized) CCA, (sparse) PLS regression, PCA and (sparse) Regularized generalised CCA</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_plotvar_script.R
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18 --input_rdata $input_rdata
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19 $adv.legend
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20 --cutoff $adv.cutoff
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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="cutoff" type="float" value="0" min="0" max="1"
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33 label="Cut-off"
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34 help="Only selected variables whose correlation with the first or second axis is greater than Cut-off in absolute value will be plotted." />
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35 </section>
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36 </inputs>
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37
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38 <outputs>
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39 <data name="output_pdf" format="pdf" label="plotVar.pdf" />
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40 </outputs>
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42 <tests>
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43 <test>
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44 <param name="input_rdata" value="out_rdata.rdata" />
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45 <output name="output_pdf" value="out_plotVar.pdf" />
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46 </test>
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47 </tests>
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49 <help>
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50 <![CDATA[
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51 .. class:: infomark
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52
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53 **Authors** Pierre Pericard (pierre.pericard@pasteur-lille.fr)
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54
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55 ---------------------------------------------------
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56
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57 .. class:: infomark
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58
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59 **Please cite**
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60
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61 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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62 PLOS Computational Biology 13(11): e1005752. https://doi.org/10.1371/journal.pcbi.1005752
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63
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64 ---------------------------------------------------
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65
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66 ================
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67 mixOmics plotVar
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68 ================
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69
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70 -----------
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71 Description
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72 -----------
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73
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74 The plotVar function is part of the mixOmics package for exploration and integration of Omics datasets.
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75 Provides variables representation for (regularized) CCA, (sparse) PLS regression, PCA and (sparse) Regularized generalised CCA.
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76
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77 -----------
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78 Input files
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79 -----------
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80
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81 +-------------------------------+------------+
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82 | Parameter : num + label | Format |
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83 +===============================+============+
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84 | 1 : Rdata block.splsda output | Rdata |
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85 +-------------------------------+------------+
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86
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87 ----------
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88 Parameters
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89 ----------
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90
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91 Advanced options:
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92 =================
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93
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94 Plot legend
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95
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96 Cut-off
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97
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98 ------------
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99 Output files
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100 ------------
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101
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102 plotIndiv.pdf
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103 A pdf file with scatter plots for individuals
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104
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105 ]]>
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106 </help>
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107
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108 <citations>
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109 <citation type="doi">10.1371/journal.pcbi.1005752</citation>
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110 </citations>
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111
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112 </tool>