Mercurial > repos > ppericard > viscorvar

annotate mixomics_plotvar.xml @ 3:df8428358b7f draft

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit d930da2982ffb689ba4fdf7599c8971f8c52339d"
author ppericard
date Fri, 23 Oct 2020 11:26:18 +0000
parents c8533e9298e5
children d4e9f7546dfa
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1 <tool id="mixomics_plotvar" name="mixOmics plotVar" version="@TOOL_VERSION@+galaxy1" 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_LOG_EXIT@
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26 ]]></command>
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28 <inputs>
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29 <param name="input_rdata" type="data" format="rdata"
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30 label="Input RData file from (sparse)(I)PCA, (regularized)CCA, (sparse)PLS(DA) or (sparse)(R)GCCA(DA)"
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31 help="This is the RData output file from the block.splsda function." />
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32 <section name="adv" title="Advanced Options" expanded="false">
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33 <param name="legend" type="boolean" checked="true" truevalue="--legend" falsevalue=""
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34 label="Plot legend" />
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35 <param name="cutoff" type="float" value="0" min="0" max="1"
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36 label="Cut-off"
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37 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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38 </section>
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39 </inputs>
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41 <outputs>
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42 <data name="output_pdf" format="pdf" label="plotVar.pdf" />
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43 </outputs>
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45 <tests>
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46 <test>
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47 <param name="input_rdata" value="out_rdata.rdata" />
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48 <output name="output_pdf" value="out_plotVar.pdf" />
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49 </test>
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50 </tests>
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52 <help><![CDATA[
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54 @HELP_AUTHORS@
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56 ================
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57 mixOmics plotVar
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58 ================
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60 -----------
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61 Description
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62 -----------
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64 The plotVar function is part of the mixOmics package for exploration and integration of Omics datasets.
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65 Provides variables representation for (regularized) CCA, (sparse) PLS regression, PCA and (sparse) Regularized generalised CCA.
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66
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67 -----------------
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68 Workflow position
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69 -----------------
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71 **Upstream tools**
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73 ======================= =================================== ========
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74 Name Output file Format
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75 ======================= =================================== ========
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76 mixOmics.block.splsda mixomics_blocksplsda_output.RData rdata
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77 ======================= =================================== ========
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79 ---------------------------------------------------
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80
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81 -----------
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82 Input files
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83 -----------
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84
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85 +-------------------------------+------------+
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86 | Parameter : num + label | Format |
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87 +===============================+============+
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88 | 1 : Rdata block.splsda output | Rdata |
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89 +-------------------------------+------------+
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91 ----------
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92 Parameters
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93 ----------
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94
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95 Advanced options:
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96 =================
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97
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98 Plot legend
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99
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100 Cut-off
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101
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102
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103 @HELP_MANUAL@
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104
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105 ------------
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106 Output files
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107 ------------
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108
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109 plotVar.pdf
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110 A pdf file with scatter plots for variables
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111
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112 ]]></help>
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113
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114 <expand macro="citations" />
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115
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116 </tool>