--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/wgcna_eigengene_visualization.xml	Tue Aug 08 12:35:11 2017 -0400
@@ -0,0 +1,100 @@
+<tool id="wgcna_eigengene_visualization" name="WGCNA: eigengene visualization" version="1.0.0">
+    <requirements>
+        <requirement type="package" version="1.20.0">r-getopt</requirement>
+        <requirement type="package" version="1.2">r-rmarkdown</requirement>
+        <requirement type="package" version="1.8.4">r-plyr</requirement>
+        <requirement type="package" version="0.4.0">r-highcharter</requirement>
+        <requirement type="package" version="0.2">r-dt</requirement>
+        <requirement type="package" version="0.3.5">r-htmltools</requirement>
+        <requirement type="package" version="1.51">r-wgcna</requirement>
+    </requirements>
+    <description>
+        Eigengene visualization.
+    </description>
+    <stdio>
+        <regex match="Execution halted"
+               source="both"
+               level="fatal"
+               description="Execution halted." />
+        <regex match="Error in"
+               source="both"
+               level="fatal"
+               description="An undefined error occured, please check your intput carefully and contact your administrator." />
+        <regex match="Fatal error"
+               source="both"
+               level="fatal"
+               description="An undefined error occured, please check your intput carefully and contact your administrator." />
+    </stdio>
+    <command>
+        <![CDATA[
+        ## Add tools to PATH
+        export PATH=/opt/R-3.2.5/bin:\$PATH &&
+
+        Rscript '${__tool_directory__}/wgcna_eigengene_visualization_render.R'
+
+            ## 1. input data
+            -e $echo
+            -w $construct_network_workspace
+            -p '$soft_threshold_power'
+            -n $plot_genes
+
+
+            ## 2. output report and report site directory
+		    -o $wgcna_eigengene_visualization
+		    -d $wgcna_eigengene_visualization.files_path
+
+		    ## 3. Rmd templates in the tool directory
+
+                -M '${__tool_directory__}/wgcna_eigengene_visualization.Rmd'
+
+
+
+        ]]>
+    </command>
+    <inputs>
+        <param type="data" name="construct_network_workspace" format="rdata" optional="false"
+               label="R workspace from WGCNA: construct network" />
+        <param type="integer" name="soft_threshold_power" optional="true" label="Soft threshold power"
+               help="Refer to the scale independence plot from 'WGCNA: construct network' and choose an optimal soft threshold power.
+               An optimal power will be calculated automatically if no value is provided." />
+        <param type="integer" name="plot_genes" value="400" min="1" label="Number of genes" optional="false"
+               help="The number of genes that will be used. It is possible to speed up the plotting by providing a subset of
+                    genes. However, the gene dendrogram may ofter look different from dendrogram of all genes." />
+        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
+    </inputs>
+    <outputs>
+        <data name="wgcna_eigengene_visualization" format="html" label="WGCNA: eigengene visualization" />
+    </outputs>
+    <citations>
+        <citation type="bibtex">
+            @article{langfelder2008wgcna,
+            title={WGCNA: an R package for weighted correlation network analysis},
+            author={Langfelder, Peter and Horvath, Steve},
+            journal={BMC bioinformatics},
+            volume={9},
+            number={1},
+            pages={559},
+            year={2008},
+            publisher={BioMed Central}
+            }
+        </citation>
+        <citation type="bibtex">
+            @article{allaire2016rmarkdown,
+            title={rmarkdown: Dynamic Documents for R, 2016},
+            author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
+            journal={R package version 0.9},
+            volume={6},
+            year={2016}
+            }
+        </citation>
+        <citation type="bibtex">
+            @book{xie2015dynamic,
+            title={Dynamic Documents with R and knitr},
+            author={Xie, Yihui},
+            volume={29},
+            year={2015},
+            publisher={CRC Press}
+            }
+        </citation>
+    </citations>
+</tool>
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