Mercurial > repos > ppericard > viscorvar

annotate mixomics_plotvar.xml @ 4:d4e9f7546dfa draft

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 579dc54316e8ede493f86f434a87d3d7b692b023"
author ppericard
date Tue, 17 Nov 2020 13:01:44 +0000
parents c8533e9298e5
children 88c1fd2ac110
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1 <tool id="mixomics_plotvar" name="mixOmics plotVar" version="@TOOL_VERSION@+galaxy2" 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 <macros>
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6 <import>macros.xml</import>
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7 <import>macros_mixomics.xml</import>
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8 </macros>
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10 <expand macro="requirements"/>
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11 <expand macro="stdio"/>
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13 <command detect_errors="aggressive"><![CDATA[
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15 @COMMAND_RSCRIPT@/mixomics_plotvar.R
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17 --input_rdata $input_rdata
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19 $adv.legend
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20 --cutoff $adv.cutoff
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22 --output_pdf $output_pdf
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24 ]]></command>
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26 <inputs>
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27 <param name="input_rdata" type="data" format="rdata"
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28 label="Input RData file from (sparse)(I)PCA, (regularized)CCA, (sparse)PLS(DA) or (sparse)(R)GCCA(DA)"
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29 help="this is the RData output file from the block.splsda function" />
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30 <section name="adv" title="Advanced Options" expanded="false">
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31 <param name="legend" type="boolean" checked="true" truevalue="--legend" falsevalue=""
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32 label="Plot legend" />
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33 <param name="cutoff" type="float" value="0" min="0" max="1"
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34 label="Cut-off"
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35 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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36 </section>
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37 </inputs>
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39 <outputs>
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40 <data name="output_pdf" format="pdf" label="plotVar.pdf" />
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41 </outputs>
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43 <tests>
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44 <test>
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45 <param name="input_rdata" value="out_rdata.rdata" />
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46 <output name="output_pdf" value="out_plotVar.pdf" />
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47 </test>
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48 </tests>
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50 <help><![CDATA[
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52 @HELP_AUTHORS@
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54 ================
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55 mixOmics plotVar
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56 ================
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58 -----------
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59 Description
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60 -----------
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61
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62 This tool allows visualizing the variables of a omics dataset which are correlated with the variables
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63 of the other omic datasets and the response variable in a correlation circle.
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65 -----------------
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66 Workflow position
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67 -----------------
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69 **Upstream tools**
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71 ======================= =================================== ========
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72 Name Output file Format
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73 ======================= =================================== ========
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74 mixOmics.block.splsda mixomics_blocksplsda_output.RData rdata
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75 ======================= =================================== ========
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77 ---------------------------------------------------
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78
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79 -----------
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80 Input files
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81 -----------
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83 +-------------------------------+------------+
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84 | Parameter : num + label | Format |
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85 +===============================+============+
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86 | 1 : Rdata block.splsda output | Rdata |
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87 +-------------------------------+------------+
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89 ----------
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90 Parameters
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91 ----------
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92
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93 Advanced options:
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94 =================
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95
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96 Plot legend
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97
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98 Cut-off
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99
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100
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101 @HELP_MANUAL@
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102
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103 ------------
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104 Output files
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105 ------------
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106
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107 plotVar.pdf
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108 A pdf file with scatter plots for variables
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109
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110 ]]></help>
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111
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112 <expand macro="citations" />
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113
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114 </tool>