Mercurial > repos > mingchen0919 > rmarkdown_samtools_flagstat

diff rmarkdown_samtools_flagstat.xml @ 4:ec39bfeaf496 draft

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update
author mingchen0919
date Wed, 27 Dec 2017 15:14:47 -0500
parents 106ab5f33970
children 1c16536c70f5
line wrap: on
line diff
--- a/rmarkdown_samtools_flagstat.xml	Wed Dec 27 12:03:33 2017 -0500
+++ b/rmarkdown_samtools_flagstat.xml	Wed Dec 27 15:14:47 2017 -0500
@@ -11,13 +11,13 @@
   <stdio>
     <regex source="stderr" match="XXX" level="warning" description="Check the warnings_and_errors.txt file for more details."/>
   </stdio>
-  <command><![CDATA[                    Rscript '${__tool_directory__}/tool_template_render.R'
+  <command><![CDATA[                    Rscript '${__tool_directory__}/rmarkdown_samtools_flagstat_render.R'
                         -e $echo
                         -b $input_bam
                         -r $report
                         -d $report.files_path
                         -s $sink_message
-                        -t '${__tool_directory__}/tool_template.Rmd'
+                        -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"/>