--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rmarkdown_report.xml	Sun Dec 30 12:48:14 2018 -0500
@@ -0,0 +1,111 @@
+<tool name="aurora_fastqc_site" id='aurora_fastqc_site' version="2.2.1">
+    <description>
+        Evaluate short reads with FastQC software on a single or a paired of untrimmed and trimmed reads
+        files.
+    </description>
+    <requirements>
+        <requirement type="package" version="2.5">pandoc</requirement>
+        <requirement type="package" version="1.20.2">r-getopt</requirement>
+        <requirement type="package" version="1.10">r-rmarkdown</requirement>
+        <requirement type="package" version="1.8.4">r-plyr</requirement>
+        <requirement type="package" version="1.3.1">r-stringr</requirement>
+        <requirement type="package" version="0.4">r-dt</requirement>
+        <requirement type="package" version="1.4.3">r-reshape2</requirement>
+        <requirement type="package" version="4.8.0">r-plotly</requirement>
+        <requirement type="package" version="0.3.6">r-htmltools</requirement>
+        <requirement type="package" version="0.11.5">fastqc</requirement>
+        <requirement type="package" version="0.9.10">xorg-libxrender</requirement>
+        <requirement type="package" version="1.2.3">xorg-libsm</requirement>
+        <requirement type="package" version="6.0">unzip</requirement>
+    </requirements>
+    <stdio>
+        <regex match="XXX" source="stderr" level="warning"
+               description="Check the warnings_and_errors.txt file for more details."/>
+    </stdio>
+    <command><![CDATA[
+
+        ######### each aurora tool generates a html file and have an files path directory associated with it.
+        mkdir -p $report.files_path &&
+
+        ######### three important paths:
+        #########   1. path to tool installation directory
+        #########   2. path to report html
+        #########   3. path to files_path directory associated with the report output.
+        export TOOL_INSTALL_DIR='${__tool_directory__}' &&
+        export REPORT='$report' &&
+        export REPORT_FILES_PATH='$report.files_path' &&
+
+        ############ copy jstree directory cp -r ${__tool_directory__}/vakata-jstree-3.3.5 ./ &&
+
+        ############ create a hidden file to store r markdown rendering log
+        touch $report.files_path/.r_rendering.log.txt &&
+
+        Rscript '${__tool_directory__}/rmarkdown_report_render.R'
+
+		    -o $report
+		    -d $report.files_path
+
+		    -r $reads_1
+            -n '$reads_1.name'
+            -R $reads_2
+            -N '$reads_2.name'
+            -c $contaminants
+            -l $limits
+
+    ]]></command>
+    <inputs>
+        <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="reads_1" type="data" optional="false"
+               label="Short reads before trimming"
+               help="Short reads data from history. This could be reads before trimming."/>
+        <param format="fastq,fastq.gz,fastq.bz2,bam,sam" name="reads_2" type="data" label="Short reads after trimming"
+               help="Short reads data from history. This could be reads after trimming."/>
+        <param name="contaminants" type="data" format="tabular" optional="true" label="Contaminant list"
+               help="Specifies a non-default file which contains the list of adapter sequences which will be explicitly
+               searched against the library. The file must contain sets of named adapters in the form name[tab]sequence.
+               Lines prefixed with a hash will be ignored."/>
+        <param name="limits" type="data" format="txt" optional="true" label="Submodule and Limit specifing file"
+               help="Specifies a non-default file which contains a set of criteria which will be used to determine the
+               warn/error limits for the various modules. This file can also be used to selectively remove some modules
+               from the output all together. The format needs to mirror the default limits.txt file found in the
+               Configuration folder."/>
+
+    </inputs>
+    <outputs>
+        <data format="html" name="report" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <citations>
+        <citation type="bibtex"><![CDATA[
+            @online{jstree,
+            author={Bozhanov, Ivan},
+            year = 2018,
+            url = {https://www.jstree.com/}
+            }
+        ]]></citation>
+        <citation type="bibtex"><![CDATA[
+            @misc{bioinformatics2014fastqc,
+            title={FastQC},
+            author={Bioinformatics, Babraham},
+            year={2014}
+            }
+        ]]></citation>
+        <citation type="bibtex"><![CDATA[
+            @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"><![CDATA[
+            @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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