# HG changeset patch
# User mingchen0919
# Date 1514522010 18000
# Node ID 80a4b509a055de910e09b3ef428f5538f557d2d6
# Parent  cbddfddabf29b2e210303105e6c70a5998df0b39
update

diff -r cbddfddabf29 -r 80a4b509a055 rmarkdown_feature_counts.xml
--- a/rmarkdown_feature_counts.xml	Thu Dec 28 22:45:35 2017 -0500
+++ b/rmarkdown_feature_counts.xml	Thu Dec 28 23:33:30 2017 -0500
@@ -74,9 +74,9 @@
         <param type="text" name="gtf_attr_type" label="GTF.attrType"
                help="a character string giving the attribute type in the GTF annotation which will be used to group features (eg. exons) into meta-features (eg. genes). gene_id by default. This argument is only applicable when isGTFAnnotationFile is TRUE"
                optional="False" value="gene_id"/>
-        <param type="text" name="chr_aliases" label="chrAliases"
+        <param type="data" name="chr_aliases" label="chrAliases"
                help="a character string giving the name of a file that contains aliases of chromosome names. The file should be a comma delimited text file that includes two columns. The first column gives the chromosome names used in the annotation and the second column gives the chromosome names used by reads. This file should not contain header lines. Names included in this file are case sensitive."
-               optional="False"/>
+               optional="True" format="csv"/>
         <param type="boolean" name="use_meta_features" label="useMetaFeatures"
                help="logical indicating whether the read summarization should be performed at the feature level (eg. exons) or meta-feature level (eg genes). If TRUE, features in the annotation (each row is a feature) will be grouped into meta-features using their values in the &quot;GeneID&quot; column in the SAF-format annotation file or using the &quot;gene_id&quot; attribute in the GTF-format annotation file, and reads will assiged to the meta-features instead of the features. See below for more details."
                optional="False" truevalue="TRUE" falsevalue="FALSE"/>
diff -r cbddfddabf29 -r 80a4b509a055 rmarkdown_feature_counts_render.R
--- a/rmarkdown_feature_counts_render.R	Thu Dec 28 22:45:35 2017 -0500
+++ b/rmarkdown_feature_counts_render.R	Thu Dec 28 23:33:30 2017 -0500
@@ -33,38 +33,39 @@
   args_list=list()
   ##------- 1. input data ---------------------
   args_list$ECHO = c('echo', 'e', '1', 'character')
-  args_list$b = c('input_bam', 'b', '1', 'character')
+  args_list$a = c('input_bam', 'a', '1', 'character')
+  args_list$b = c('annot_built', 'b', '1', 'character')
   args_list$c = c('annot_ext', 'c', '1', 'character')
   args_list$f = c('isGTFAnnotationFile', 'f', '1', 'character')
   args_list$g = c('gtf_feature_type', 'g', '1', 'character')
   args_list$h = c('gtf_attr_type', 'h', '1', 'character')
-  args_list$i = c('chr_aliases', 'i', '1', 'character')
+  args_list$i = c('chr_aliases', 'i', '2', 'character')
   args_list$j = c('use_meta_features', 'j', '1', 'character')
   args_list$k = c('allow_multi_overlap', 'k', '1', 'character')
-  args_list$l = c('min_overlap', 'l', '1', 'character')
+  args_list$l = c('min_overlap', 'l', '1', 'integer')
   args_list$m = c('largest_overlap', 'm', '1', 'character')
-  args_list$n = c('read_extension_5', 'n', '1', 'character')
-  args_list$o = c('read_extension_3', 'o', '1', 'character')
+  args_list$n = c('read_extension_5', 'n', '1', 'integer')
+  args_list$o = c('read_extension_3', 'o', '1', 'integer')
   args_list$p = c('read_2_pos', 'p', '1', 'character')
   args_list$q = c('count_multi_mapping_reads', 'q', '1', 'character')
   args_list$u = c('fraction', 'u', '1', 'character')
-  args_list$v= c('min_mqs', 'v', '1', 'character')
+  args_list$v= c('min_mqs', 'v', '1', 'integer')
   args_list$w= c('split_only', 'w', '1', 'character')
   args_list$x= c('non_split_only', 'x', '1', 'character')
   args_list$y= c('primary_only', 'y', '1', 'character')
   args_list$z= c('ignore_dup', 'z', '1', 'character')
-  args_list$A= c('strand_specific', 'A', '1', 'character')
+  args_list$A= c('strand_specific', 'A', '1', 'integer')
   args_list$B= c('junc_counts', 'B', '1', 'character')
   args_list$C= c('genome', 'C', '1', 'character')
   args_list$D= c('is_paired_end', 'D', '1', 'character')
   args_list$E= c('require_both_ends_mapped', 'E', '1', 'character')
   args_list$F= c('check_frag_length', 'F', '1', 'character')
-  args_list$G= c('min_frag_length', 'G', '1', 'character')
-  args_list$H= c('max_frag_length', 'H', '1', 'character')
+  args_list$G= c('min_frag_length', 'G', '1', 'integer')
+  args_list$H= c('max_frag_length', 'H', '1', 'integer')
   args_list$I= c('count_chimeric_fragments', 'I', '1', 'character')
   args_list$J= c('auto_sort', 'J', '1', 'character')
-  args_list$K= c('n_threads', 'K', '1', 'character')
-  args_list$L= c('max_mop', 'L', '1', 'character')
+  args_list$K= c('n_threads', 'K', '1', 'integer')
+  args_list$L= c('max_mop', 'L', '1', 'integer')
   args_list$M= c('report_reads', 'M', '1', 'character')
   
   ##--------2. output report and outputs --------------