diff README.rst @ 3:d7ce95ccf54f

Change R data file format in xml wrappers (rda -> RData) Add test data, sample workflow. Updated README with instructions on testing.

--- a/README.rst	Tue Jul 21 15:40:22 2015 +0100
+++ b/README.rst	Wed Jul 22 12:07:39 2015 +0100
@@ -1,11 +1,11 @@
 riboseqr_wrapper
-----------------
+================
 `riboSeqR <http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html>`_
 integration for `Galaxy <http://galaxyproject.org/>`_ and
 `RiboGalaxy <http://ribogalaxy.ucc.ie/>`_.
 
 Included tools
-..............
+--------------
 In the order they are run
 
 1. Prepare riboSeqR Input - Prepare riboSeqR format input files from SAM format alignment files.
@@ -24,13 +24,48 @@
    translation analysis with baySeq.
 
 Dependencies
-............
-Tested on Ubuntu Linux 14.04 LTS, 64-bit. Dependencies should install automatically on Linux x86_64.
+------------
+Tested on Ubuntu Linux 14.04 LTS, 64-bit. Dependencies should install automatically on Linux 64-bit.
+
+R ``3.1.2``, riboSeqR ``1.0.5``, baySeq ``2.0.50``, rpy2 ``2.3.10``.
+
+How to test
+-----------
+1. Upload the following test data files from the test-data folder.
+
+   Prepare riboSeqR input (R data file)
 
-**R** ``3.1.2``
+   rsem_chlamy236_deNovo.transcripts.fa
+
+2. A workflow with test data is included in this repository. All tools with the exception of "Prepare riboSeqR input"
+   can currently be tested using this workflow. Import this workflow into Galaxy.
+
+3. Run workflow
+
+   In Step 1 of the workflow, select "Prepare riboSeqR input (R data file)" as input.
+
+   In Step 2, select rsem_chlamy236_deNovo.transcripts.fa as input.
 
-**riboSeqR** ``1.0.5``
+   Run workflow.
+
+
+About the test data files
+.........................
+The included "Prepare riboSeqR input (R data file)" is saved from an R session using sample data included with the
+riboSeqR package. The commands used were ::
+
+   library(riboSeqR)
 
-**baySeq** ``2.0.50``
+   datadir <- system.file("extdata", package = "riboSeqR")
+   chlamyFasta <- paste(datadir, "/rsem_chlamy236_deNovo.transcripts.fa", sep = "")
+
+   fastaCDS <- findCDS(fastaFile = chlamyFasta, startCodon = c("ATG"), stopCodon = c("TAG", "TAA", "TGA"))
 
-**rpy2** ``2.3.10``
+   ribofiles <- paste(datadir, "/chlamy236_plus_deNovo_plusOnly_Index", c(17,3,5,7), sep = "")
+   rnafiles <- paste(datadir, "/chlamy236_plus_deNovo_plusOnly_Index", c(10,12,14,16), sep = "")
+
+   riboDat <- readRibodata(ribofiles, rnafiles, replicates = c("WT", "WT", "M", "M"))
+   save(riboDat, file="Prepare riboSeqR input (R data file)")
+
+rsem_chlamy236_deNovo.transcripts.fa - sample data from the riboSeqR package.
+