annotate pcaFactoMineR.xml @ 0:7acfb3bdad66 draft default tip

planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556

<!--# Copyright (C) 2017 INRA
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
# 
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see http://www.gnu.org/licenses/.
#-->

<tool id="pcafactominer" name="PCAFactoMineR" version="1.0.0">
    <description>Realize a PCA analysis using FactoMineR package</description>
    <requirements>
        <requirement type="package" version="1.38" >r-factominer</requirement>
        <requirement type="package">r-base</requirement>
        <requirement type="package">bioconductor-pcamethods</requirement>
        <requirement type="package">r-batch</requirement>
    </requirements>
    <stdio>
        <!-- Anything other than zero is an error -->
        <exit_code range="1:" level="fatal" />
        <exit_code range=":-1" level="fatal" />
    </stdio>
    <command interpreter="Rscript"><![CDATA[
        pcaFactoMineR_galaxy.R
        datafile '${datafile}'
        npc '${npc}'
        #if str( $condPlot.plotOptions ) == "yes":

          plotev '${condPlot.plotev}'
          plotcontrib '${condPlot.plotcontrib}'
          plotindiv '${condPlot.condScore.plotindiv}'

          #if str( $condPlot.condScore.plotindiv ) == "yes":
            colorfactor '${condPlot.condScore.condColor.colorfactor}'
            #if str( $condPlot.condScore.condColor.colorfactor ) == "yes":
              samplemetadata '${condPlot.condScore.condColor.samplemetadata}'
              factor '${condPlot.condScore.condColor.factor}'
            #else :
              samplemetadata "None"
              factor "None"
            #end if
          #else :
            colorfactor yes
            samplemetadata "None"
            factor "None"
          #end if

          plotvar '${condPlot.condLoading.plotvar}'

          #if str( $condPlot.condLoading.plotvar ) == "yes":
            contribh '${condPlot.condLoading.contribh}'
            contribv '${condPlot.condLoading.contribv}'
          #else :
            contribh 0
            contribv 0
          #end if

        #else :
          plotev yes
          plotcontrib yes
          plotindiv yes
          colorfactor no
          samplemetadata "None"
          factor "None"
          plotvar yes
          contribh 0
          contribv 0
        #end if

        #if str( $condGraphical.graphicalOptions ) == "yes":
          title '${condGraphical.title}'
          pch '${condGraphical.pch}'
          pcv '${condGraphical.pcv}'
          tc '${condGraphical.tc}'
        #else :
          title "PCA" 
          pch 1
          pcv 2
          tc 1
        #end if
        varinline '${varinline}'

        ## Outputs
        logOut '${log_file}'
        outgraphpdf '${output_file}'
    ]]></command>
    <inputs>
        <param name="datafile" type="data" label="Data matrix" help="Precise below if the variable are in line or column" format="tabular,csv" />
        <param name="npc" label="Number of principal components" type="integer" value="2" min="2" help="" />
        <conditional name="condPlot">
            <param name="plotOptions" type="select" label="Plot Options" help="If no, it will create the 4 plot and take the default parameters">
                <option value="no" selected="true">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="yes">
                <param name="plotev" type="select" label="Eigenvalue plot" help="Eigenvalue and percentage of explained variance plots">
                    <option value="yes" selected="true"> Yes </option>
                    <option value="no"> No </option>
                </param>
                <param name="plotcontrib" type="select" label="Contribution plot" help="">
                    <option value="yes" selected="true"> Yes </option>
                    <option value="no"> No </option>
                </param>
                <conditional name="condScore">
                    <param name="plotindiv" label="Score plot" type="select" help="">
                        <option value="yes" selected="true"> Yes </option>
                        <option value="no"> No </option>
                    </param>
                    <when value="yes">
                        <conditional name="condColor">
                            <param name="colorfactor" label="Factor color" type="select" help="Colouring of observations according to levels of qualitative variable (biological factor of interest)">
                                <option value="no" selected="true"> No </option>
                                <option value="yes"> Yes </option>
                            </param>
                            <when value="yes">
                                <param name="samplemetadata" type="data" label="Factor file" help="File with Biological Factor(s)" format="tabular,csv" />
                                <param name="factor" label="Name of the column of the factor matrix corresponding to the qualitative variable" type="text" value="None" help="" />
                            </when>
                            <when value="no"></when>
                        </conditional>
                    </when>
                    <when value="no"></when>
                </conditional>
                <conditional name="condLoading">
                    <param name="plotvar" label="Loading plot" type="select" help="">
                        <option value="yes" selected="true"> Yes </option>
                        <option value="no"> No </option>
                    </param>
                    <when value="yes">
                        <param name="contribh" label="Contribution threshold (abscissa)" type="float" value="0" help="Contribution threshold for loading plot (Principal component displayed in the abscissa axis)" />
                        <param name="contribv" label="Contribution threshold (ordinate)" type="float" value="0" help="Contribution threshold for loading plot (Principal component displayed in the ordinate axis)" />
                    </when>
                    <when value="no"></when>
                </conditional>
            </when>
            <when value="no"></when>
        </conditional>
        <conditional name="condGraphical">
            <param name="graphicalOptions" type="select" label="GraphicalOptions" help="If not, it will take the default parameters">
                <option value="no" selected="true">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="yes">
                <param name="title" type="text" label="Title" help="Title printed on all plots; if none, leave 'PCA'" value="PCA" />
                <param name="pch" label="Horizontal Principal Component" type="integer" value="1" help="Principal component displayed on the abscissa" />
                <param name="pcv" label="Vertical Principal Component" help="Principal component displayed on the ordinate" type="integer" value="2" />
                <param name="tc" label="Numeric character expansion factor" type="float" value="1.0" min="0.5" help="A value greater than 1 increases and a value lower than 1 decreases character size" />
            </when>
            <when value="no"></when>
        </conditional>
        <param name="varinline" type="select" multiple="false" display="radio" label="Variable in line or column?">
            <option value="yes">Line</option>
            <option value="no">Column</option>
        </param>
    </inputs>
    <outputs>
        <data name="log_file" format="html" label="${tool.name}_log" />
        <data name="output_file" label="${tool.name}_graph" format="pdf" />
    </outputs>
    <tests>
        <test>
            <param name="datafile" value="decathlon.tsv"/>
            <param name="npc" value="2"/>
            <conditional name="condPlot">
                <param name="plotOptions" value="no"/>
            </conditional>
            <conditional name="condGraphical">
                <param name="graphicalOptions" value="no"/>
            </conditional>
            <param name="varinline" value="no"/>
            <output name="log_file" file="log_file"/>
            <output name="output_file" file="output_file" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
	
===
PCA
===

-----------
Description
-----------

 - This tool is part of a set of statistical tools made by members of the BIOS4BIOL group ("Normalization", "Summary statistics", "Hierarchical clustering" and "PCAFactoMineR").
 - Please use the Normalization module that come with the suite before using this module.

What it does:
 - Principal Component Analysis (PCA) as done in the FactoMineR package

------

-----------
Input files
-----------

+---------------------------+------------+
| Parameter : num + label   |   Format   |
+===========================+============+
| 1 : data matrix           |   tabular  |
+---------------------------+------------+

----------
Parameters
----------

Data matrix
	| see "Input files" section above
	| 

Number of principal component
	| How many principal components include in the PCA model?
	|

(?)Plot options
        | Show (or not) more options for the plots
        |

Eigenvalue plot
	| Eigenvalue and percentage of explained variance plots. Default value is "Yes"
	|

Contribution plot
	| Contribution plot. Default value is "Yes"
	|

Score plot
	| Score plot" plot. Default value is "Yes"
	|

Factor color	
	| Colouring of observations. Default value is "Yes"
	|

Factor file
	| File containing the biological factor (qualitative variable) to color observations according to levels of this
	|

Factor
	| Name of the column containing the biological factor 
	|

Loading plot
	| Loading plot. Default value is "Yes"
	|

Contribution threshold (abscissa)
	| Contribution threshold for loading plot: principal component displayed in the abscissa axis
	|

Contribution threshold (ordinate)
	| Contribution threshold for loading plot: principal component displayed in the ordinate axis
	|

(?)Graphical options
        | Show (or not) more graphical options
        |

Title
	| Title printed on all plots; if none, leave 'PCA'" value="PCA"
	|

Numeric character expansion factor 
	| A value greater than 1 increases and a value lower than 1 decreases character size
	|

Horizontal Principal Component
	| Principal component displayed on the abscissa
	|

Vertical Principal Component
	| Principal component displayed on the ordinate
	|

Variable Line/Column
        | Variable in line or in column in the input file. Default value is "Line" 
        |

------------
Output files
------------

PCAFactoMineR_graph (pdf output)
	| 

PCAFactoMineR_log 
	| 

------

**Authors** Marie Tremblay-Franco ([e-mail]), Jean-Francois Martin ([e-mail]), Sandrine Laguerre ([e-mail]) and Valentin Marcon ([e-mail])

Contact : [e-mail]

E-learning available : Not yet.

.. class:: infomark

-------------
Please cite :
-------------

- (Depending on the help provided you can cite us in acknowledgements, references or both.)
    
Acknowledgements
        | We wish to thank the SIGENAE group and the statistical CATI BIOS4Biol group : Marie Tremblay-Franco, Jean-Francois Martin, Sandrine Laguerre.
        | Re-packaging was provided by Valentin Marcon (INRA, Migale platform http://migale.jouy.inra.fr), as part of the IFB project 'Galaxy For Life Science' (http://www.france-bioinformatique.fr/fr)
        | 
    
References
        | SIGENAE [http://www.sigenae.org/]
        |
 
    ]]></help>
    <citations>
        <citation type="bibtex">
        @article{10.18637/jss.v025.i01,
        title = {{FactoMineR}: A Package for Multivariate Analysis},
        author = {S\'ebastien Le and Julie Josse and Fran\c{c}ois Husson},
        journal = {Journal of Statistical Software},
        year = {2008},
        volume = {25},
        number = {1},
        pages = {1--18},
        doi = {10.18637/jss.v025.i01},
        url = {https://dx.doi.org/10.18637/jss.v025.i01}}
        </citation>
    </citations>
</tool>