changeset 3:106ab5f33970 draft

fix input type error

--- a/rmarkdown_samtools_flagstat.xml	Wed Dec 27 11:58:37 2017 -0500
+++ b/rmarkdown_samtools_flagstat.xml	Wed Dec 27 12:03:33 2017 -0500
@@ -11,24 +11,24 @@
   <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><![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"/>
   </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>
-  <help><![CDATA[<code>samtools flagstat in.sam|in.bam|in.cram</code>
-
+  <help><![CDATA[<code>samtools flagstat in.sam|in.bam|in.cram</code>
+
 Does a full pass through the input file to calculate and print statistics to stdout]]></help>
   <citations>
     <citation><![CDATA[
@@ -40,15 +40,15 @@
                         volume={6},
                         year={2016}
                     ]]></citation>
-    <citation type="bibtex"><![CDATA[@article{li2009sequence,
-  title={The sequence alignment/map format and SAMtools},
-  author={Li, Heng and Handsaker, Bob and Wysoker, Alec and Fennell, Tim and Ruan, Jue and Homer, Nils and Marth, Gabor and Abecasis, Goncalo and Durbin, Richard},
-  journal={Bioinformatics},
-  volume={25},
-  number={16},
-  pages={2078--2079},
-  year={2009},
-  publisher={Oxford University Press}
+    <citation type="bibtex"><![CDATA[@article{li2009sequence,
+  title={The sequence alignment/map format and SAMtools},
+  author={Li, Heng and Handsaker, Bob and Wysoker, Alec and Fennell, Tim and Ruan, Jue and Homer, Nils and Marth, Gabor and Abecasis, Goncalo and Durbin, Richard},
+  journal={Bioinformatics},
+  volume={25},
+  number={16},
+  pages={2078--2079},
+  year={2009},
+  publisher={Oxford University Press}
 }]]></citation>
   </citations>
 </tool>