comparison rmarkdown_samtools_flagstat.xml @ 4:ec39bfeaf496 draft

update

3:106ab5f33970

  </requirements>
  <description>simple stats on BAM file</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
                        -b $input_bam
                        -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_bam" label="BAM file" optional="False"/>
  </inputs>

4:ec39bfeaf496

  </requirements>
  <description>simple stats on BAM file</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__}/rmarkdown_samtools_flagstat_render.R'
                        -e $echo
                        -b $input_bam
                        -r $report
                        -d $report.files_path
                        -s $sink_message
                        -t '${__tool_directory__}/rmarkdown_samtools_flagstat.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_bam" label="BAM file" optional="False"/>
  </inputs>