# HG changeset patch
# User mingchen0919
# Date 1514497769 18000
# Node ID a8ddefbaf55e4157c89ebccc6962d14babfbf2cb
# Parent  36fc6d325d1be8347e162cd1053dba8500870011
update

diff -r 36fc6d325d1b -r a8ddefbaf55e rmarkdown_feature_counts.xml
--- a/rmarkdown_feature_counts.xml	Thu Dec 28 09:51:14 2017 -0500
+++ b/rmarkdown_feature_counts.xml	Thu Dec 28 16:49:29 2017 -0500
@@ -13,16 +13,19 @@
                description="Check the warnings_and_errors.txt file for more details."/>
     </stdio>
     <command><![CDATA[
-                    Rscript '${__tool_directory__}/tool_template_render.R'
+                    Rscript '${__tool_directory__}/rmarkdown_feature_counts_render.R'
                         -e $echo
                         -r $report
                         -d $report.files_path
                         -s $sink_message
-                        -t '${__tool_directory__}/tool_template.Rmd'
+                        -t '${__tool_directory__}/rmarkdown_feature_counts.Rmd'
                     ]]></command>
     <inputs>
         <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/SAM files"
+               help="The files can be in either SAM format or BAM format. The file format is automatically detected by the function"
+               optional="False" format="bam,sam" multiple="True"/>
         <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"/>
@@ -54,10 +57,10 @@
                optional="False" checked="True" truevalue="TRUE" falsevalue="FALSE"/>
         <param type="integer" name="read_extension_5" label="readExtension5"
                help="integer giving the number of bases extended upstream from 5' end of each read. 0 by default."
-               optional="False" value="0"/>
+               optional="False" value="1"/>
         <param type="integer" name="read_extension_3" label="readExtension3"
                help="integer giving the number of bases extended downstream from 3' end of each read. 0 by default."
-               optional="False" value="0"/>
+               optional="False" value="1"/>
         <param type="text" name="read_2_pos" label="read2pos"
                help="Specifying whether each read should be reduced to its 5' most base or 3' most base. It has three possible values: NULL, 5 (denoting 5' most base) and 3 (denoting 3' most base). The default value is NULL. With the default value, the whole read is used for summarization. When read2pos is set to 5 (or 3), read summarization will be performed based on the 5' (or 3') most base position. read2pos can be used together with readExtension5 and readExtension3 parameters to set any desired length for reads."
                optional="False" value="NULL"/>
@@ -69,7 +72,7 @@
                optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
         <param type="integer" name="min_mqs" label="minMQS"
                help="integer giving the minimum mapping quality score a read must satisfy in order to be counted. For paired-end reads, at least one end should satisfy this criteria. 0 by default."
-               optional="False" value="0"/>
+               optional="False"/>
         <param type="boolean" name="split_only" label="splitOnly"
                help="logical indicating whether only split alignments (their CIGAR strings contain letter 'N') should be included for summarization. FALSE by default. Example split alignments are exon-spanning reads from RNA-seq data. useMetaFeatures should be set to FALSE and allowMultiOverlap should be set to TRUE, if the purpose of summarization is to assign exon-spanning reads to all their overlapping exons."
                optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
@@ -84,7 +87,7 @@
                optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
         <param type="integer" name="strand_specific" label="strandSpecific"
                help="integer indicating if strand-specific read counting should be performed. It has three possible values: 0 (unstranded), 1 (stranded) and 2 (reversely stranded). 0 by default."
-               optional="False" value="0"/>
+               optional="False"/>
         <param type="boolean" name="junc_counts" label="juncCounts"
                help="integer indicating if strand-specific read counting should be performed. It has three possible values: 0 (unstranded), 1 (stranded) and 2 (reversely stranded). 0 by default."
                optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>