diff mixomics_plotvar.xml @ 0:d0b77b926863 draft

"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 85dac6b13a9adce48b47b2b8cb28d2319ae9c1ca-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mixomics_plotvar.xml	Tue Jun 23 19:57:35 2020 -0400
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+<tool id="mixomics_plotvar" name="mixOmics plotVar" version="1.0" profile="16.04" workflow_compatible="true">
+
+    <description>provides variables representation for (regularized) CCA, (sparse) PLS regression, PCA and (sparse) Regularized generalised CCA</description>
+
+    <requirements>
+        <requirement type="package" version="6.12">bioconductor-mixomics</requirement>
+        <requirement type="package" version="2.0">r-argparse</requirement>
+    </requirements>
+
+    <stdio>
+        <!-- <exit_code range="1:" level="fatal" /> -->
+    </stdio>
+
+    <command detect_errors="aggressive">
+        <![CDATA[
+        Rscript
+        ${__tool_directory__}/mixomics_plotvar_script.R
+        --input_rdata $input_rdata
+        $adv.legend
+        --cutoff $adv.cutoff
+        --output_pdf $output_pdf
+        ]]>
+    </command>
+
+    <inputs>
+        <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)"
+               help="This is the RData output file from the block.splsda function." />
+        <section name="adv" title="Advanced Options" expanded="false">
+            <param name="legend" type="boolean" checked="true" truevalue="--legend" falsevalue=""
+                   label="Plot legend" />
+            <param name="cutoff" type="float" value="0" min="0" max="1"
+                   label="Cut-off"
+                   help="Only selected variables whose correlation with the first or second axis is greater than Cut-off in absolute value will be plotted." />
+        </section>
+    </inputs>
+
+    <outputs>
+        <data name="output_pdf" format="pdf" label="plotVar.pdf" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input_rdata" value="out_rdata.rdata" />
+            <output name="output_pdf" value="out_plotVar.pdf" />
+        </test>
+    </tests>
+
+    <help>
+        <![CDATA[
+.. class:: infomark
+
+**Authors** Pierre Pericard ([e-mail])
+
+---------------------------------------------------
+
+.. class:: infomark
+
+**Please cite**
+
+Rohart F, Gautier B, Singh A, Lê Cao KA (2017) mixOmics: An R package for ‘omics feature selection and multiple data integration.
+PLOS Computational Biology 13(11): e1005752. https://doi.org/10.1371/journal.pcbi.1005752
+
+---------------------------------------------------
+
+================
+mixOmics plotVar
+================
+
+-----------
+Description
+-----------
+
+The plotVar function is part of the mixOmics package for exploration and integration of Omics datasets.
+Provides variables representation for (regularized) CCA, (sparse) PLS regression, PCA and (sparse) Regularized generalised CCA.
+
+-----------
+Input files
+-----------
+
++-------------------------------+------------+
+| Parameter : num + label       |   Format   |
++===============================+============+
+| 1 : Rdata block.splsda output |   Rdata    |
++-------------------------------+------------+
+
+----------
+Parameters
+----------
+
+Advanced options:
+=================
+
+Plot legend
+
+Cut-off
+
+------------
+Output files
+------------
+
+plotIndiv.pdf
+    A pdf file with scatter plots for individuals
+
+        ]]>
+    </help>
+
+    <citations>
+        <citation type="doi">10.1371/journal.pcbi.1005752</citation>
+    </citations>
+
+</tool>
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