comparison extract_fields.xml @ 5:fc9043b919b1 draft

initial tool

4:e1d225154d4a

  <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
                        -A $field_numbers
                        -B $input_txt
                        -O $output_txt
                        -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"/>
    <param type="text" name="field_numbers" label="Field numbers" optional="False"/>
    <param type="data" name="input_txt" label="Input text file" optional="False" format="txt"/>
  </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"/>
    <param type="data" name="output_txt" label="Output text file" optional="False" format="txt"/>
  </outputs>
  <help><![CDATA[some help text]]></help>
  <citations>
    <citation type="bibtex"><![CDATA[
                    @article{allaire2016rmarkdown,

5:fc9043b919b1

  <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
                        -A $input_field_numbers
                        -B $input_txt
                        -O $output_txt
                        -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"/>
    <param type="text" name="input_field_numbers" label="input field numbers" optional="False"/>
    <param type="data" name="input_txt" label="Input text file" optional="False" format="txt"/>
  </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,