--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/wgcna_preprocessing.xml	Tue Aug 08 12:35:11 2017 -0400
@@ -0,0 +1,96 @@
+<tool id="wgcna_preprocessing" name="WGCNA: preprocessing" 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>
+        Data clearning and preprocessing.
+    </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_preprocessing_render.R'
+
+            ## 1. input data
+            -e $echo
+            -E $expression_data
+
+
+            ## 2. output report and report site directory
+		    -o $wgcna_preprocessing
+		    -d $wgcna_preprocessing.files_path
+		    -w $preprocessing_workspace
+
+		    ## 3. Rmd templates sitting in the tool directory
+
+		        ## _site.yml and index.Rmd template files
+                -D '${__tool_directory__}/wgcna_preprocessing.Rmd'
+
+
+
+        ]]>
+    </command>
+    <inputs>
+        <param type="data" name="expression_data" format="csv" optional="false" label="Gene expression data"
+               help="Each row represents a gene and each column represents a sample."/>
+
+        <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
+    </inputs>
+    <outputs>
+        <data name="wgcna_preprocessing" format="html" label="WGCNA: preprocessing" />
+        <data name="preprocessing_workspace" format="rdata" label="R workspace: WGCNA preprocessing" />
+    </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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