Mercurial > repos > peterjc > rxlr_venn_workflow
diff README.rst @ 4:3c280e01b920 draft
Uploaded v0.0.2, bump tool version numbers to fix warning about Filter1 parameter, adding link to Tool Shed in annotation. No functional changes.
author | peterjc |
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date | Wed, 21 Aug 2013 13:01:51 -0400 |
parents | 1a1ab2f2b5b5 |
children | 4726b640f221 |
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--- a/README.rst Mon Aug 19 11:35:52 2013 -0400 +++ b/README.rst Wed Aug 21 13:01:51 2013 -0400 @@ -5,6 +5,30 @@ See http://www.galaxyproject.org for information about the Galaxy Project. +Sample Data +=========== + +This workflow was developed and run on several Phytophthora species. +For example, try the "Phyca11" protein set for Phytophthora capsici: + +http://genome.jgi-psf.org/Phyca11/download/Phyca11_filtered_proteins.fasta.gz + +You can upload this directly into Galaxy via this URL. Galaxy will handle +removing the gzip compression to give you the FASTA protein file which +has 19,805 protein sequences. The expected results: + +* 89 RXLRs using Whisson et al. (2007) +* 124 RXLRs using Win et al. (2007) +* 162 RXLRs using Bhattacharjee et al. (2006) + +Of these, only 79 sequences pass all three of the RXLR prediction tools, +while 19643 have no RXLR matches at all. + +.. image:: https://raw.github.com/peterjc/picobio/master/galaxy_workflows/rxlr_venn_workflow/Phyca11_example_output.png + :height: 400px + :width: 400px + + Citation ======== @@ -63,6 +87,21 @@ HMMER v2.0, and the R/Bioconductor package limma). +History +======= + +======= ====================================================================== +Version Changes +------- ---------------------------------------------------------------------- +v0.0.1 - Initial release to Tool Shed (May, 2013) + - Expanded README file to include example data +v0.0.2 - Updated versions of the tools used, inclulding core Galaxy Filter + tool to avoid warning about new ``header_lines`` parameter. + - Added link to Tool Shed in the workflow annotation explaining there + is a README file with sample data, and a requested citation. +======= ====================================================================== + + Developers ==========