Mercurial > repos > ppericard > mixomics_blocksplsda

annotate mixomics_plotvar.xml @ 1:6595c17673cb draft

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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7ed137ea956b8074c34d43a5e1d46b39ddef1482-dirty
author ppericard
date Wed, 12 Jun 2019 11:22:33 -0400
parents bea08702ed51
children 655d1fbcd3e6
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bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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1 <tool id="mixomics_plotvar" name="mixOmics plotVar" version="0.1.0" 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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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" label="Input RData file from (sparse)(I)PCA, (regularized)CCA, (sparse)PLS(DA) or (sparse)(R)GCCA(DA)"/>
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27 <section name="adv" title="Advanced Options" expanded="false">
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28 <param name="legend" type="boolean" checked="true" truevalue="--legend" falsevalue="" label="Plot legend"/>
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29 <param name="cutoff" type="float" value="0" min="0" max="1" label="Cut-off" />
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30 </section>
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31 </inputs>
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33 <outputs>
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34 <data name="output_pdf" format="pdf" label="plotVar.pdf" />
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35 </outputs>
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37 <tests>
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38 <test>
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39 <param name="input_rdata" value="out_rdata.rdata" />
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40 <output name="output_pdf" value="out_plotVar.pdf" />
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41 </test>
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42 </tests>
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44 <help>
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45 <![CDATA[
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46 .. class:: infomark
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47
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48 **Authors** Pierre Pericard (pierre.pericard@pasteur-lille.fr)
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50 ---------------------------------------------------
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51
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52 .. class:: infomark
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53
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54 **Please cite**
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55
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56 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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57 PLOS Computational Biology 13(11): e1005752. https://doi.org/10.1371/journal.pcbi.1005752
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58
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59 ---------------------------------------------------
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61 ================
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62 mixOmics plotVar
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63 ================
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64
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65 -----------
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66 Description
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67 -----------
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68
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69 The plotVar function is part of the mixOmics package for exploration and integration of Omics datasets.
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70 Provides variables representation for (regularized) CCA, (sparse) PLS regression, PCA and (sparse) Regularized generalised CCA.
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71
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72 -----------
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73 Input files
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74 -----------
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75
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76 +-------------------------------+------------+
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77 | Parameter : num + label | Format |
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78 +===============================+============+
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79 | 1 : Rdata block.splsda output | Rdata |
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80 +-------------------------------+------------+
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81
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82 ----------
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83 Parameters
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84 ----------
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85
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86 Advanced options:
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87 =================
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88
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89 Plot legend
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90
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91 Cut-off
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92
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93 ------------
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94 Output files
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95 ------------
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96
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97 plotIndiv.pdf
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98 A pdf file with scatter plots for individuals
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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99
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100 ]]>
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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101 </help>
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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102
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103 <citations>
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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104 <citation type="doi">10.1371/journal.pcbi.1005752</citation>
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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105 </citations>
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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106
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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107 </tool>