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comparison README.rst @ 2:3a0c0d1c388f draft

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Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
author peterjc
date Wed, 21 Aug 2013 11:58:54 -0400
parents 606da4e1d925
children 72f03c2102ee
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1:606da4e1d925 2:3a0c0d1c388f
2 secreted proteins from a given protein FASTA file. 2 secreted proteins from a given protein FASTA file.
3 3
4 It runs SignalP v3.0 (Bendtsen et al. 2004) and selects only proteins with a 4 It runs SignalP v3.0 (Bendtsen et al. 2004) and selects only proteins with a
5 strong predicted signal peptide, and then runs TMHMM v2.0 (Krogh et al. 2001) 5 strong predicted signal peptide, and then runs TMHMM v2.0 (Krogh et al. 2001)
6 on those, and selects only proteins without a predicted trans-membrane helix. 6 on those, and selects only proteins without a predicted trans-membrane helix.
7 This workflow was used in Kikuchi et al (2001), and is a simplification of 7 This workflow was used in Kikuchi et al. (2011), and is a simplification of
8 the candidate effector protocol described in Jones et al (2009). 8 the candidate effector protocol described in Jones et al. (2009).
9 9
10 See http://www.galaxyproject.org for information about the Galaxy Project. 10 See http://www.galaxyproject.org for information about the Galaxy Project.
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13 Sample Data
14 ===========
15
16 This workflow was developed and run on several nematode species. For example,
17 try the protein set for Bursaphelenchus xylophilus (Kikuchi et al. 2011):
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19 ftp://ftp.sanger.ac.uk/pub/pathogens/Bursaphelenchus/xylophilus/Assembly-v1.2/BUX.v1.2.genedb.protein.fa.gz
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21 You can upload this directly into Galaxy via this URL. Galaxy will handle
22 removing the gzip compression to give you the FASTA protein file which has
23 18,074 sequences. The expected result (selecting organism type Eukaryote)
24 is a FASTA protein file of 2,297 predicted secreted protein sequences.
11 25
12 26
13 Citation 27 Citation
14 ======== 28 ========
15 29
76 However, at the time of writing those Galaxy tools have their own 90 However, at the time of writing those Galaxy tools have their own
77 dependencies required for this workflow which require manual 91 dependencies required for this workflow which require manual
78 installation (SignalP v3.0 and TMHMM v2.0). 92 installation (SignalP v3.0 and TMHMM v2.0).
79 93
80 94
95 History
96 =======
97
98 ======= ======================================================================
99 Version Changes
100 ------- ----------------------------------------------------------------------
101 v0.0.1 - Initial release to Tool Shed (May, 2013)
102 - Expanded README file to include example data
103 v0.0.2 - Updated versions of the tools used, inclulding core Galaxy Filter
104 tool to avoid warning about new ``header_lines`` parameter.
105 ======= ======================================================================
106
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81 Developers 108 Developers
82 ========== 109 ==========
83 110
84 This workflow is under source code control here: 111 This workflow is under source code control here:
85 112