view extract_fields.xml @ 8:ac0c560845dc draft

initial tool

<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'

                        -A $input_field_numbers
                        -B $input_file
                        -O $output_txt
                    ]]></command>
  <inputs>
    <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
    <param type="text" name="input_field_numbers" optional="False"/>
    <param type="data" name="input_file" optional="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"/>
    <data name="output_txt" format="txt" hidden="false"/>
  </outputs>
  <help><![CDATA[some help text]]></help>
  <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>
  </citations>
</tool>