diff README.rst @ 6:5a242f289347 default tip

Merge

--- a/README.rst	Tue Oct 27 12:21:50 2015 +0000
+++ b/README.rst	Tue Oct 27 12:29:39 2015 +0000
@@ -1,22 +1,13 @@
-README
-------
-
+riboseqr_wrapper
+================
 `riboSeqR <http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html>`_
-integration for `Galaxy <http://galaxyproject.org/>`_ /
-`RiboGalaxy <http://ribogalaxy.ucc.ie/>`_.
+integration for `RiboGalaxy <http://ribogalaxy.ucc.ie/>`_ and `Galaxy <http://galaxyproject.org/>`_.
 
 Included tools
-..............
-In the order in which they are run
-
-#. Prepare riboSeqR Input
+--------------
+In the order they are run
 
-   Prepare riboSeqR format input files from alignment files (SAM format,
-   Ribo-Seq or RNA-Seq alignments).
-
-#. Triplet Periodicity
-
-   Plot triplet periodicity for different read lengths.
+#. Plot triplet periodicity for different read lengths.
 
 #. Metagene Analysis
 
@@ -33,12 +24,52 @@
    Get Ribo and RNA-Seq counts with riboSeqR. Perform differential
    translation analysis with baySeq.
 
-Tested with
-...........
-**R** ``3.1.2``
+Dependencies
+------------
+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)
+
+   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.
+
+   Run workflow.
 
-**riboSeqR** ``1.0.5``
+
+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)
+
+   datadir <- system.file("extdata", package = "riboSeqR")
+   chlamyFasta <- paste(datadir, "/rsem_chlamy236_deNovo.transcripts.fa", sep = "")
 
-**baySeq** ``2.0.50``
+   fastaCDS <- findCDS(fastaFile = chlamyFasta, startCodon = c("ATG"), stopCodon = c("TAG", "TAA", "TGA"))
+
+   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 = "")
 
-**rpy2** ``2.3.10``
+   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.
+
+Bugs/Issues?
+------------
+Please report here https://github.com/vimalkumarvelayudhan/riboseqr_wrapper/issues