diff aurora_data.xml @ 0:ebb7afcb2b75 draft default tip

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/aurora_data.xml	Tue Apr 17 10:58:55 2018 -0400
@@ -0,0 +1,51 @@
+<tool id="aurora_data" name="aurora_data" version="1.0.0">
+    <description>Collect data for other aurora galaxy tools.</description>
+    <requirements>
+        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
+        <requirement type="package" version="1.20.0">r-getopt</requirement>
+        <requirement type="package" version="1.6">r-rmarkdown</requirement>
+    </requirements>
+    <stdio>
+        <regex match="XXX" source="stderr" level="warning"
+               description="Check the warnings_and_errors.txt file for more details."/>
+    </stdio>
+    <command><![CDATA[
+        export TOOL_DIR='${__tool_directory__}' &&
+
+        Rscript '${__tool_directory__}/rmarkdown_report_render.R'
+
+			-o $report
+			-d $report.files_path
+        
+    ]]></command>
+    <inputs>
+        <repeat name="data_repeat" title="data" min="1" default="1">
+            <param type="data" name="data" label="Data from history" optional="False"/>
+            <param type="text" name="data_name" label="data name" optional="False" help="data name has to be unique."/>
+        </repeat>
+    </inputs>
+    <outputs>
+        <data name="report" format="html" label="${tool.name} on ${on_string}" hidden="false"/>
+    </outputs>
+    <citations>
+        <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>