Mercurial > repos > mingchen0919 > one_command_liners

changeset 0:953c4ff00986 draft

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planemo upload
author mingchen0919
date Sun, 18 Feb 2018 23:36:03 -0500
parents
children da18ae80603c
files extract_fields.xml
diffstat 1 files changed, 40 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_fields.xml	Sun Feb 18 23:36:03 2018 -0500
@@ -0,0 +1,40 @@
+<tool id="tool_template" name="tool name" version="1.0.0">
+  <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="1.3">r-rmarkdown</requirement>
+    <requirement type="package" version="0.3.5">r-htmltools</requirement>
+    <requirement type="package" version="0.5.0">r-dplyr</requirement>
+  </requirements>
+  <description>some descriptions about the tool.</description>
+  <stdio>
+    <regex source="stderr" match="XXX" level="warning" description="Check the warnings_and_errors.txt file for more details."/>
+  </stdio>
+  <command><![CDATA[
+                    Rscript '${__tool_directory__}/tool_template_render.R'
+                        -e $echo
+                        -r $report
+                        -d $report.files_path
+                        -s $sink_message
+                        -t '${__tool_directory__}/tool_template.Rmd'
+                    ]]></command>
+  <inputs>
+    <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
+  </inputs>
+  <outputs>
+    <data name="report" format="html" label="tool name report" hidden="false"/>
+    <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" hidden="false"/>
+  </outputs>
+  <help><![CDATA[some help text]]></help>
+  <citations>
+    <citation><![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>
+  </citations>
+</tool>