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comparison rmarkdown_flagstat.xml @ 1:c5c626653593 draft

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fix wrong input type error
author mingchen0919
date Tue, 26 Dec 2017 20:42:47 -0500
parents ba913054bbff
children
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0:ba913054bbff 1:c5c626653593
9 </requirements> 9 </requirements>
10 <description>Descriptive stats for BAM dataset</description> 10 <description>Descriptive stats for BAM dataset</description>
11 <stdio> 11 <stdio>
12 <regex source="stderr" match="XXX" level="warning" description="Check the warnings_and_errors.txt file for more details."/> 12 <regex source="stderr" match="XXX" level="warning" description="Check the warnings_and_errors.txt file for more details."/>
13 </stdio> 13 </stdio>
14 <command><![CDATA[ 14 <command><![CDATA[ Rscript '${__tool_directory__}/tool_template_render.R'
15 Rscript '${__tool_directory__}/tool_template_render.R'
16 -e $echo 15 -e $echo
16 -b $input_bam
17 -r $report 17 -r $report
18 -d $report.files_path 18 -d $report.files_path
19 -s $sink_message 19 -s $sink_message
20 -t '${__tool_directory__}/tool_template.Rmd 20 -t '${__tool_directory__}/tool_template.Rmd
21 ]]></command> 21 ]]></command>
22 <inputs> 22 <inputs>
23 <param type="integer" name="echo" label="Display analysis code in report?" optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/> 23 <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
24 <param type="data" name="input_bam" label="BAM file" optional="False" format="bam"/> 24 <param type="data" name="input_bam" label="BAM file" optional="False" format="bam"/>
25 </inputs> 25 </inputs>
26 <outputs> 26 <outputs>
27 <data name="report" format="html" label="tool name report" hidden="false"/> 27 <data name="report" format="html" label="tool name report" hidden="false"/>
28 <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" hidden="false"/> 28 <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" hidden="false"/>