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comparison README.rst @ 4:3c280e01b920 draft

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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
date Wed, 21 Aug 2013 13:01:51 -0400
parents 1a1ab2f2b5b5
children 4726b640f221
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3:1a1ab2f2b5b5 4:3c280e01b920
1 This is package is a Galaxy workflow for comparing three RXLR prediction 1 This is package is a Galaxy workflow for comparing three RXLR prediction
2 methods with a Venn Diagram, and creates a FASTA file of any proteins 2 methods with a Venn Diagram, and creates a FASTA file of any proteins
3 passing all three methods. 3 passing all three methods.
4 4
5 See http://www.galaxyproject.org for information about the Galaxy Project. 5 See http://www.galaxyproject.org for information about the Galaxy Project.
6
7
8 Sample Data
9 ===========
10
11 This workflow was developed and run on several Phytophthora species.
12 For example, try the "Phyca11" protein set for Phytophthora capsici:
13
14 http://genome.jgi-psf.org/Phyca11/download/Phyca11_filtered_proteins.fasta.gz
15
16 You can upload this directly into Galaxy via this URL. Galaxy will handle
17 removing the gzip compression to give you the FASTA protein file which
18 has 19,805 protein sequences. The expected results:
19
20 * 89 RXLRs using Whisson et al. (2007)
21 * 124 RXLRs using Win et al. (2007)
22 * 162 RXLRs using Bhattacharjee et al. (2006)
23
24 Of these, only 79 sequences pass all three of the RXLR prediction tools,
25 while 19643 have no RXLR matches at all.
26
27 .. image:: https://raw.github.com/peterjc/picobio/master/galaxy_workflows/rxlr_venn_workflow/Phyca11_example_output.png
28 :height: 400px
29 :width: 400px
6 30
7 31
8 Citation 32 Citation
9 ======== 33 ========
10 34
61 However, at the time of writing those Galaxy tools have their own dependencies 85 However, at the time of writing those Galaxy tools have their own dependencies
62 required for this workflow which require manual installation (SignalP v3.0, 86 required for this workflow which require manual installation (SignalP v3.0,
63 HMMER v2.0, and the R/Bioconductor package limma). 87 HMMER v2.0, and the R/Bioconductor package limma).
64 88
65 89
90 History
91 =======
92
93 ======= ======================================================================
94 Version Changes
95 ------- ----------------------------------------------------------------------
96 v0.0.1 - Initial release to Tool Shed (May, 2013)
97 - Expanded README file to include example data
98 v0.0.2 - Updated versions of the tools used, inclulding core Galaxy Filter
99 tool to avoid warning about new ``header_lines`` parameter.
100 - Added link to Tool Shed in the workflow annotation explaining there
101 is a README file with sample data, and a requested citation.
102 ======= ======================================================================
103
104
66 Developers 105 Developers
67 ========== 106 ==========
68 107
69 This workflow is under source code control here: 108 This workflow is under source code control here:
70 109