diff rmarkdown_feature_counts.xml @ 7:7857bfd9d604 draft

update

--- a/rmarkdown_feature_counts.xml	Thu Dec 28 16:56:01 2017 -0500
+++ b/rmarkdown_feature_counts.xml	Thu Dec 28 22:07:13 2017 -0500
@@ -15,6 +15,40 @@
     <command><![CDATA[
                     Rscript '${__tool_directory__}/rmarkdown_feature_counts_render.R'
                         -e $echo
+                        -a $input_bam
+                        -b $annot_inbuilt
+                        -c '$annot_ext'
+                        -f $isGTFAnnotationFile
+                        -g $gtf_feature_type
+                        -h $gtf_attr_type
+                        -i $chr_aliases
+                        -j $use_meta_features
+                        -k $allow_multi_overlap
+                        -l $min_overlap
+                        -m $largest_overlap
+                        -n $read_extension_5
+                        -o $read_extension_3
+                        -p $read_2_pos
+                        -q $count_multi_mapping_reads
+                        -u $fraction
+                        -v $min_mqs
+                        -w $split_only
+                        -x $non_split_only
+                        -y $primary_only
+                        -z $ignore_dup
+                        -A $strand_specific
+                        -B $junc_counts
+                        -C $genome
+                        -D $is_paired_end
+                        -E $require_both_ends_mapped
+                        -F $check_frag_length
+                        -G $min_frag_length
+                        -H $max_frag_length
+                        -I $count_chimeric_fragments
+                        -J $auto_sort
+                        -K $n_threads
+                        -L $max_mop
+                        -M $report_reads
                         -r $report
                         -d $report.files_path
                         -s $sink_message