comparison extract_fields.xml @ 2:f1f549e6d0bc draft

initial tool

1:da18ae80603c

  </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>

2:f1f549e6d0bc

  </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
                        -i  $input_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="data" name="input_txt" 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"/>
  </outputs>