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

planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556

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+++ b/pcaFactoMineR.xml	Thu Jan 18 07:57:36 2018 -0500
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+<!--# 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>