# HG changeset patch
# User mingchen0919
# Date 1514471910 18000
# Node ID 50abf2092001bba360b9104477499a2c5851aaeb
# Parent  8bcae2a95fe740f67e864b5c2f0204b520f6105f
create tool

diff -r 8bcae2a95fe7 -r 50abf2092001 rmarkdown_feature_counts.xml
--- a/rmarkdown_feature_counts.xml	Thu Dec 28 09:29:15 2017 -0500
+++ b/rmarkdown_feature_counts.xml	Thu Dec 28 09:38:30 2017 -0500
@@ -21,12 +21,7 @@
                     ]]></command>
   <inputs>
     <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
-    <param type="select" name="annot_inbuilt" optional="False" multiple="False">
-      <option value="mm10" selected="true" XML_value="mm10"/>
-      <option value="mm9" selected="false"/>
-      <option value="hg38" selected="false"/>
-      <option value="hg19" selected="false"/>
-    </param>
+    <param type="text" name="annot_inbuilt" label="annot.inbuilt" help="a character string specifying an in-built annotation used for read summarization. It has four possible values including mm10, mm9, hg38 and hg19, corresponding to the NCBI RefSeq annotations for genomes 'mm10', 'mm9', 'hg38' and 'hg19', respectively. mm10 by default. The in-built annotation has a SAF format (see below)." optional="False" value="mm10"/>
     <param type="data" name="annot_ext" label="External annotation (GTF)" help="A character string giving name of a user-provided annotation file or a data frame including user-provided annotation data" optional="False" format="gtf,saf" multiple="False"/>
     <param type="boolean" name="isGTFAnnotationFile" optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
     <param type="text" name="gtf_feature_type" label="GTF.featureType" help="a character string giving the feature type used to select rows in the GTF annotation which will be used for read summarization. exon by default. This argument is only applicable when isGTFAnnotationFile is TRUE" optional="False" value="exon"/>