--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/wgcna_construct_network.xml	Tue Aug 08 12:35:50 2017 -0400
@@ -0,0 +1,105 @@
+<tool id="wgcna_construct_network" name="WGCNA: construct network" 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>
+        Construct gene network.
+    </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[
+
+        Rscript '${__tool_directory__}/wgcna_construct_network_render.R'
+
+            ## 1. input data
+            -e $echo
+            -w $preprocessing_workspace
+            -h '$height_cut'
+            -t $trait_data
+
+
+
+            ## 2. output report and report site directory
+		    -o $wgcna_construct_network
+		    -d $wgcna_construct_network.files_path
+		    -W $construct_network_workspace
+
+
+		    ## 3. Rmd templates in the tool directory
+
+		        ## _site.yml and index.Rmd template files
+                -M '${__tool_directory__}/wgcna_construct_network.Rmd'
+
+
+
+        ]]>
+    </command>
+    <inputs>
+        <param type="data" name="preprocessing_workspace" format="rdata" optional="false"
+               label="R workspace from WGCNA: preprocessing" />
+        <param type="float" name="height_cut" optional="true" label="Height"
+               help="Refer to the sample clustering plot from WGCNA: preprocessing and choose a height cut that will
+                    remove outliers. If there is not outlier, leave this field blank." />
+        <param type="data" name="trait_data" format="csv" optional="true"
+               label="Trait data"
+               help="If trait data is provided, a plot consisting of sample clustering and trait heatmap will
+                    be generated. This field is optional. "/>
+
+        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
+    </inputs>
+    <outputs>
+        <data name="wgcna_construct_network" format="html" label="WGCNA: construct_network" />
+        <data name="construct_network_workspace" format="rdata" label="R workspace: WGCNA construct_network" />
+    </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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