--- a/readme.rst	Mon Aug 12 12:56:19 2013 -0400
+++ b/readme.rst	Fri Aug 23 02:54:15 2013 -0400
@@ -1,28 +1,108 @@
-==============================
-Glimmer3 gene calling workflow
-==============================
+This package is a Galaxy workflow for gene prediction using Glimmer3.
+
+It uses the Glimmer3 tool (Delcher et al. 2007) trained on a known set of
+genes to generate gene predictions on a new genome, and then calls EMBOSS
+(Rice et al. 2000) to translate the predictions into a FASTA file of
+predicted protein sequences. The workflow requires two input files:
+
+* Nucleotide FASTA file of know gene sequences (training set)
+* Nucleotide FASTA file of genome sequence or assembled contigs
+
+First an interpolated context model (ICM) is built from the set of known
+genes, preferably from the closest relative organism(s) available. Next this
+ICM model is used to predict genes on the genomic FASTA file. This produces
+a FASTA file of the predicted gene nucleotide sequences, which is translated
+into protein sequences using the EMBOSS tool transeq.
+
+Glimmer is intended for finding genes in microbial DNA, especially bacteria,
+archaea, and viruses.
+
+See http://www.galaxyproject.org for information about the Galaxy Project.
 
-This Tool Shed Repository contains a workflow for the gene prediction of from a given nucleotide FASTA file.
+
+Sample Data
+===========
+
+As an example, we will use the first public assembly of the 2011 Shiga-toxin
+producing *Escherichia coli* O104:H4 outbreak in Germany. This was part of the
+open-source crowd-sourcing analysis described in Rohde et al. (2011) and here:
+https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/wiki
 
-At first an interpolated context model (ICM) is build from a know set of genes, preferable from the closest relative available organism(s). In a following step this ICM model is used to predict genes on the second input. The output is a FASTA file with nucleotide sequences that is further converted to proteins sequences.
+You can upload this assembly directly into Galaxy using the "Upload File" tool
+with either of these URLs - Galaxy should recognise this is a FASTA file with
+3,057 sequences:
 
-To run that worflow glimmer_ und the EMBOSS_ suite is required. Both can be installed from the Tool Shed.
+* http://static.xbase.ac.uk/files/results/nick/TY2482/TY2482.fasta.txt
+* https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/blob/master/strains/TY2482/seqProject/BGI/assemblies/NickLoman/TY2482.fasta.txt
+
+This FASTA file ``TY2482.fasta.txt`` was the initial TY-2482 strain assembled
+by Nick Loman from 5 runs of Ion Torrent data released by the BGI, using the
+MIRA 3.2 assembler. It was initially released via his blog,
+http://pathogenomics.bham.ac.uk/blog/2011/06/ehec-genome-assembly/
 
-.. _glimmer: http://www.cbcb.umd.edu/software/glimmer/
-.. _EMBOSS: http://emboss.sourceforge.net/
+We will also need a training set of known *E. coli* genes, for example the
+model strain *Escherichia coli* str. K-12 substr. MG1655 which is well
+annotated. You can upload the NCBI FASTA file ``NC_000913.ffn`` of the
+gene nucleotide sequences directly into Galaxy via this URL, which Galaxy
+should recognise as a FASTA file with 4,321 sequences:
+
+* ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__MG1655_uid57779/NC_000913.ffn
+
+Then run the workflow, which should produce 2,333 predicted genes for the
+TY2482 assembly (two FASTA files, nucleotide and protein sequences).
+
 
-| A. L. Delcher, K.A. Bratke, E.C. Powers, and S.L. Salzberg. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (Advance online version) (2007).
+Citation
+========
+
+If you use this workflow directly, or a derivative of it, or the associated
+Glimmer wrappers for Galaxy, in work leading to a scientific publication,
+please cite:
+
+Cock, P.J.A., Grüning, B., Paszkiewicz, K. and Pritchard, L. (2013)
+Galaxy tools and workflows for sequence analysis with applications in
+molecular plant pathology. (Submitted).
+
+For Glimmer3 please cite:
 
-EMBOSS: The European Molecular Biology Open Software Suite (2000) 
-Rice,P. Longden,I. and Bleasby,A. 
-Trends in Genetics 16, (6) pp276--277
+Delcher, A.L., Bratke, K.A., Powers, E.C., and Salzberg, S.L. (2007)
+Identifying bacterial genes and endosymbiont DNA with Glimmer.
+Bioinformatics 23(6), 673-679.
+http://dx.doi.org/10.1093/bioinformatics/btm009
+
+For EMBOSS please cite:
+
+Rice, P., Longden, I. and Bleasby, A. (2000)
+EMBOSS: The European Molecular Biology Open Software Suite
+Trends in Genetics 16(6), 276-277.
+http://dx.doi.org/10.1016/S0168-9525(00)02024-2
 
-************
+
+Additional References
+=====================
+
+Rohde, H., Qin, J., Cui, Y., Li, D., Loman, N.J., et al. (2011)
+Open-source genomic analysis of shiga-toxin-producing E. coli O104:H4.
+New England Journal of Medicine 365, 718-724.
+http://dx.doi.org/10.1056/NEJMoa1107643
+
+
 Availability
-************
+============
 
 This workflow is available on the main Galaxy Tool Shed:
+
 http://toolshed.g2.bx.psu.edu/view/bgruening/glimmer_gene_calling_workflow
 
 Development is being done on github:
+
 https://github.com/bgruening/galaxytools/workflows/glimmer3/
+
+
+Dependencies
+============
+
+These dependencies should be resolved automatically via the Galaxy Tool Shed:
+
+* http://toolshed.g2.bx.psu.edu/view/bgruening/glimmer3
+* http://toolshed.g2.bx.psu.edu/view/devteam/emboss_5