# HG changeset patch
# User mingchen0919
# Date 1514338967 18000
# Node ID c5c62665359355889612454eaaed4980bfda97a6
# Parent  ba913054bbffd77888148db3f005cab3c9ee7810
fix wrong input type error

diff -r ba913054bbff -r c5c626653593 rmarkdown_flagstat.xml
--- a/rmarkdown_flagstat.xml	Tue Dec 26 19:27:41 2017 -0500
+++ b/rmarkdown_flagstat.xml	Tue Dec 26 20:42:47 2017 -0500
@@ -11,16 +11,16 @@
   <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><![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="integer" name="echo" label="Display analysis code in report?" optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
+    <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" format="bam"/>
   </inputs>
   <outputs>