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annotate README.txt @ 2:e99b1bbe44f8 draft

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Line-wrap the README file for display on the Tool Shed
author peterjc
date Tue, 07 May 2013 13:54:45 -0400
parents e21be67dbc91
children 65d174589251
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1 This Tool Shed Repository contains a workflow for comparing three RXLR
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2 prediction methods with a Venn Diagram, and creates a FASTA file of any
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3 proteins passing all three methods.
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6 References
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7 ==========
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9 Stephen C. Whisson, Petra C. Boevink, Lucy Moleleki, Anna O. Avrova,
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10 Juan G. Morales, Eleanor M. Gilroy, Miles R. Armstrong, Severine Grouffaud,
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11 Pieter van West, Sean Chapman, Ingo Hein, Ian K. Toth, Leighton Pritchard
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12 and Paul R. J. Birch A translocation signal for delivery of oomycete
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13 effector proteins into host plant cells. Nature 450:115-118, 2007.
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14 http://dx.doi.org/10.1038/nature06203
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16 Joe Win, William Morgan, Jorunn Bos, Ksenia V. Krasileva, Liliana M. Cano,
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17 Angela Chaparro-Garcia, Randa Ammar, Brian J. Staskawicz and Sophien Kamoun.
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18 Adaptive evolution has targeted the C-terminal domain of the RXLR effectors
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19 of plant pathogenic oomycetes. The Plant Cell 19:2349-2369, 2007.
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20 http://dx.doi.org/10.1105/tpc.107.051037
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22 Souvik Bhattacharjee, N. Luisa Hiller, Konstantinos Liolios, Joe Win,
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23 Thirumala-Devi Kanneganti, Carolyn Young, Sophien Kamoun and Kasturi Haldar.
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24 The malarial host-targeting signal is conserved in the Irish potato famine
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25 pathogen. PLoS Pathogens, 2(5):e50, 2006.
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26 http://dx.doi.org/10.1371/journal.ppat.0020050
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29 Availability
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30 ============
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31
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32 This workflow is available on the main Galaxy Tool Shed:
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33 http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow
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35 Development is being done on github here:
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36 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow
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39 Dependencies
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40 ============
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41
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42 These dependencies should be resolved automatically via the Galaxy Tool Shed:
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43 * http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
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44 * http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
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45 * http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list
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46
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47 However, at the time of writing those Galaxy tools have their own dependencies
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48 required for this workflow which require manual installation (SignalP v3.0,
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49 HMMER v2.0, and the R/Bioconductor package limma).