diff rmarkdown_feature_counts.xml @ 11:238d57ce7d74 draft

update

--- a/rmarkdown_feature_counts.xml	Fri Dec 29 00:17:31 2017 -0500
+++ b/rmarkdown_feature_counts.xml	Fri Dec 29 14:07:35 2017 -0500
@@ -5,6 +5,7 @@
         <requirement type="package" version="1.3">r-rmarkdown</requirement>
         <requirement type="package" version="0.3.5">r-htmltools</requirement>
         <requirement type="package" version="0.5.0">r-dplyr</requirement>
+        <requirement type="package" version="0.2">r-dt</requirement>
         <requirement type="package" version="1.25.2">bioconductor-rsubread</requirement>
     </requirements>
     <description>This function assigns mapped sequencing reads to genomic features</description>
@@ -15,7 +16,18 @@
     <command><![CDATA[
                     Rscript '${__tool_directory__}/rmarkdown_feature_counts_render.R'
                         -e $echo
-                        -a $input_bam
+                        ##----- code chunk to get file paths and raw file names for a multiple inputs data field ----
+                        #set $sep = ''
+                        #set $input_bam_paths = ''
+                        #set $input_bam_names = ''
+                        #for $input_bam in $input_bams:
+                            #set $input_bam_paths += $sep + str($input_bam)
+                            #set $input_bam_names += $sep + str($input_bam.name)
+                            #set $sep = ','
+                        #end for
+                        ##----------------- end for getting file names and file paths ------------------------------
+                        -a '$input_bam_paths'
+                        -N '$input_bam_names'
                         -b $annot_inbuilt
                         -c '$annot_ext'
                         -f $isGTFAnnotationFile
@@ -57,7 +69,7 @@
     <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"
+        <param type="data" name="input_bams" 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"
@@ -163,10 +175,14 @@
         <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"/>
+        <data name="feature_counts" format="rdata" label="feature counts" from_work_dir="feature_counts.RData"
+              hidden="false"/>
+        <data name="feature_counts_csv" format="csv" label="feature counts in csv" from_work_dir="feature_counts.csv"
+              hidden="false"/>
     </outputs>
     <help><![CDATA[some help text]]></help>
     <citations>
-        <citation><![CDATA[
+        <citation type="bibtex"><![CDATA[
                     @article{allaire2016rmarkdown,
                         title={rmarkdown: Dynamic Documents for R, 2016},
                         author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff