Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/rxlr_motifs.xml @ 25:41a42022f815 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded v0.2.6, embedded citations
author peterjc
date Fri, 21 Nov 2014 08:17:36 -0500
parents 90e3d02f8013
children 20139cb4c844
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 22
diff changeset
1 <tool id="rxlr_motifs" name="RXLR Motifs" version="0.0.9">
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
2 <description>Find RXLR Effectors of Plant Pathogenic Oomycetes</description>
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
3 <command interpreter="python">
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 22
diff changeset
4 rxlr_motifs.py "$fasta_file" "\$GALAXY_SLOTS" $model "$tabular_file"
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
5 </command>
7
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
6 <stdio>
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
7 <!-- Anything other than zero is an error -->
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
8 <exit_code range="1:" />
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
9 <exit_code range=":-1" />
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
10 </stdio>
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
11 <inputs>
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
12 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences" />
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
13 <param name="model" type="select" label="Which RXLR model?">
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
14 <option value="Bhattacharjee2006">Bhattacharjee et al. (2006) RXLR</option>
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
15 <option value="Win2007">Win et al. (2007) RXLR</option>
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
16 <option value="Whisson2007" selected="True">Whisson et al. (2007) RXLR-EER with HMM</option>
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
17 </param>
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
18 </inputs>
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
19 <outputs>
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
20 <data name="tabular_file" format="tabular" label="$model.value_label" />
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
21 </outputs>
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
22 <requirements>
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
23 <!-- Need SignalP for all the models -->
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
24 <requirement type="binary">signalp</requirement>
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
25 <!-- Need HMMER for Whisson et al. (2007) -->
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
26 <requirement type="binary">hmmsearch</requirement>
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
27 </requirements>
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
28 <tests>
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
29 <test>
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
30 <param name="fasta_file" value="rxlr_win_et_al_2007.fasta" ftype="fasta" />
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
31 <param name="model" value="Win2007" />
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
32 <output name="tabular_file" file="rxlr_win_et_al_2007.tabular" ftype="tabular" />
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
33 </test>
18
2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools
peterjc
parents: 17
diff changeset
34 <test>
2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools
peterjc
parents: 17
diff changeset
35 <param name="fasta_file" value="empty.fasta" ftype="fasta"/>
2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools
peterjc
parents: 17
diff changeset
36 <param name="model" value="Bhattacharjee2006"/>
2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools
peterjc
parents: 17
diff changeset
37 <output name="tabular_file" file="empty_rxlr.Bhattacharjee2006.tabular" ftype="tabular"/>
2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools
peterjc
parents: 17
diff changeset
38 </test>
2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools
peterjc
parents: 17
diff changeset
39 <test>
2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools
peterjc
parents: 17
diff changeset
40 <param name="fasta_file" value="empty.fasta" ftype="fasta"/>
2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools
peterjc
parents: 17
diff changeset
41 <param name="model" value="Win2007"/>
2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools
peterjc
parents: 17
diff changeset
42 <output name="tabular_file" file="empty_rxlr.Win2007.tabular" ftype="tabular"/>
2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools
peterjc
parents: 17
diff changeset
43 </test>
2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools
peterjc
parents: 17
diff changeset
44 <test>
2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools
peterjc
parents: 17
diff changeset
45 <param name="fasta_file" value="empty.fasta" ftype="fasta"/>
2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools
peterjc
parents: 17
diff changeset
46 <param name="model" value="Whisson2007"/>
2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools
peterjc
parents: 17
diff changeset
47 <output name="tabular_file" file="empty_rxlr.Whisson2007.tabular" ftype="tabular"/>
2b35b5c4b7f4 Uploaded v0.2.5, preview 2, fixed bug in RXLR tools
peterjc
parents: 17
diff changeset
48 </test>
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
49 </tests>
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
50 <help>
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
51
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
52 **Background**
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
53
7
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
54 Many effector proteins from oomycete plant pathogens for manipulating the host
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
55 have been found to contain a signal peptide followed by a conserved RXLR motif
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
56 (Arg, any amino acid, Leu, Arg), and then sometimes EER (Glu, Glu, Arg). There
7
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed
peterjc
parents: 6
diff changeset
57 are striking parallels with the malarial host-targeting signal (Plasmodium
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
58 export element, or "Pexel" for short).
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
59
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
60 -----
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
61
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
62 **What it does**
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
63
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
64 Takes a protein sequence FASTA file as input, and produces a simple tabular
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
65 file as output with one line per protein, and two columns giving the sequence
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
66 ID and the predicted class. This is typically just whether or not it had the
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
67 selected RXLR motif (Y or N).
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
68
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
69 -----
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
70
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
71 **Bhattacharjee et al. (2006) RXLR Model**
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
72
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
73 Looks for the oomycete motif RXLR as described in Bhattacharjee et al. (2006).
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
74
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
75 Matches must have a SignalP Hidden Markov Model (HMM) score of at least 0.9,
20
a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information.
peterjc
parents: 18
diff changeset
76 a SignalP Neural Network (NN) predicted cleavage site giving a signal peptide
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
77 length between 10 and 40 amino acids inclusive, and the RXLR pattern must be
20
a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information.
peterjc
parents: 18
diff changeset
78 after but within 100 amino acids of the cleavage site.
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
79 SignalP is run truncating the sequences to the first 70 amino acids, which was
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
80 the default on the SignalP webservice used in Bhattacharjee et al. (2006).
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
81
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
82
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
83 **Win et al. (2007) RXLR Model**
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
84
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
85 Looks for the protein motif RXLR as described in Win et al. (2007).
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
86
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
87 Matches must have a SignalP Hidden Markov Model (HMM) score of at least 0.9,
20
a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information.
peterjc
parents: 18
diff changeset
88 a SignalP Neural Network (NN) predicted cleavage site giving a signal peptide
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
89 length between 10 and 40 amino acids inclusive, and the RXLR pattern must be
20
a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information.
peterjc
parents: 18
diff changeset
90 after the cleavage site and start between amino acids 30 and 60.
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
91 SignalP is run truncating the sequences to the first 70 amino acids, to match
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
92 the methodology of Torto et al. (2003) followed in Win et al. (2007).
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
93
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
94
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
95 **Whisson et al. (2007) RXLR-EER with HMM**
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
96
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
97 Looks for the protein motif RXLR-EER using the heuristic regular expression
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
98 methodolgy, which was an extension of the Bhattacharjee et al. (2006) model,
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
99 and a HMM as described in Whisson et al. (2007).
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
100
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
101 All the requirements described above for Bhattacharjee et al. (2006) apply,
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
102 but rather than just looking for RXLR with the regular expression R.LR the
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
103 more complicated regular expression R.LR.{,40}[ED][ED][KR] is used. This means
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
104 RXLR (Arg, any amino acid, Leu, Arg), then a stretch of up to forty amino
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
105 acids before Glu/Asp, Glu/Asp, Lys/Arg. The EER part of the name is perhaps
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
106 misleading as it also allows for DDR, EEK, and so on.
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
107
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
108 Unlike Bhattacharjee et al. (2006) which used the SignalP webservice which
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
109 defaults to truncating the sequences at 70 amino acids, Whisson et al. (2007)
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
110 used the SignalP 3.0 command line tool with its default of not truncating the
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
111 sequences. This does alter some of the scores, and also takes a little longer.
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
112
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
113 Additionally HMMER 2.3.2 is run to look for a cross validated HMM for the
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
114 RXLR-ERR domain based on known positive examples. There are no restrictions
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
115 on where within the protein the HMM match must be found.
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
116
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
117 The output of this model has four classes:
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
118 * Y = Yes, both the heuristic motif and HMM were found.
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
119 * re = Only the heuristic SignalP with regular expression motif was found.
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
120 * hmm = Only the HMM was found.
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
121 * neither = Niether the heuristic motif nor HMM was found.
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
122
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
123 -----
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
124
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
125 **Note**
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
126
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
127 Both Bhattacharjee et al. (2006) and Win et al. (2007) used SignalP v2.0, which
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
128 is no longer available. The current release is SignalP v3.0 (Mar 5, 2007), so
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
129 this is used instead. SignalP is called with the Eukaryote model and the short
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
130 output (one line per protein). Any sequence truncation (e.g. to 70 amino acids)
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
131 is handled via the intemediate sequence files.
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
132
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
133 -----
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
134
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
135 **References**
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
136
20
a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information.
peterjc
parents: 18
diff changeset
137 If you use this Galaxy tool in work leading to a scientific publication please
a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information.
peterjc
parents: 18
diff changeset
138 cite Cock et al. (2013) and the appropriate method paper(s):
a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information.
peterjc
parents: 18
diff changeset
139
22
90e3d02f8013 Uploaded v0.2.5 preview 6, can use accents in <help> RST
peterjc
parents: 20
diff changeset
140 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
20
a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information.
peterjc
parents: 18
diff changeset
141 Galaxy tools and workflows for sequence analysis with applications
a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information.
peterjc
parents: 18
diff changeset
142 in molecular plant pathology. PeerJ 1:e167
a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information.
peterjc
parents: 18
diff changeset
143 http://dx.doi.org/10.7717/peerj.167
a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information.
peterjc
parents: 18
diff changeset
144
22
90e3d02f8013 Uploaded v0.2.5 preview 6, can use accents in <help> RST
peterjc
parents: 20
diff changeset
145 Stephen C. Whisson, Petra C. Boevink, Lucy Moleleki, Anna O. Avrova, Juan G. Morales, Eleanor M. Gilroy, Miles R. Armstrong, Severine Grouffaud, Pieter van West, Sean Chapman, Ingo Hein, Ian K. Toth, Leighton Pritchard and Paul R. J. Birch (2007).
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
146 A translocation signal for delivery of oomycete effector proteins into host plant cells.
22
90e3d02f8013 Uploaded v0.2.5 preview 6, can use accents in <help> RST
peterjc
parents: 20
diff changeset
147 Nature 450:115-118.
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
148 http://dx.doi.org/10.1038/nature06203
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
149
22
90e3d02f8013 Uploaded v0.2.5 preview 6, can use accents in <help> RST
peterjc
parents: 20
diff changeset
150 Joe Win, William Morgan, Jorunn Bos, Ksenia V. Krasileva, Liliana M. Cano, Angela Chaparro-Garcia, Randa Ammar, Brian J. Staskawicz and Sophien Kamoun (2007).
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
151 Adaptive evolution has targeted the C-terminal domain of the RXLR effectors of plant pathogenic oomycetes.
22
90e3d02f8013 Uploaded v0.2.5 preview 6, can use accents in <help> RST
peterjc
parents: 20
diff changeset
152 The Plant Cell 19:2349-2369.
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
153 http://dx.doi.org/10.1105/tpc.107.051037
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
154
22
90e3d02f8013 Uploaded v0.2.5 preview 6, can use accents in <help> RST
peterjc
parents: 20
diff changeset
155 Souvik Bhattacharjee, N. Luisa Hiller, Konstantinos Liolios, Joe Win, Thirumala-Devi Kanneganti, Carolyn Young, Sophien Kamoun and Kasturi Haldar (2006).
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
156 The malarial host-targeting signal is conserved in the Irish potato famine pathogen.
22
90e3d02f8013 Uploaded v0.2.5 preview 6, can use accents in <help> RST
peterjc
parents: 20
diff changeset
157 PLoS Pathogens, 2(5):e50.
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
158 http://dx.doi.org/10.1371/journal.ppat.0020050
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
159
22
90e3d02f8013 Uploaded v0.2.5 preview 6, can use accents in <help> RST
peterjc
parents: 20
diff changeset
160 Trudy A. Torto, Shuang Li, Allison Styer, Edgar Huitema, Antonino Testa, Neil A.R. Gow, Pieter van West and Sophien Kamoun (2003).
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
161 EST mining and functional expression assays identify extracellular effector proteins from the plant pathogen *phytophthora*.
22
90e3d02f8013 Uploaded v0.2.5 preview 6, can use accents in <help> RST
peterjc
parents: 20
diff changeset
162 Genome Research, 13:1675-1685.
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
163 http://dx.doi.org/10.1101/gr.910003
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
164
22
90e3d02f8013 Uploaded v0.2.5 preview 6, can use accents in <help> RST
peterjc
parents: 20
diff changeset
165 Sean R. Eddy (1998).
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
166 Profile hidden Markov models.
22
90e3d02f8013 Uploaded v0.2.5 preview 6, can use accents in <help> RST
peterjc
parents: 20
diff changeset
167 Bioinformatics, 14(9):755–763.
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
168 http://dx.doi.org/10.1093/bioinformatics/14.9.755
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
169
22
90e3d02f8013 Uploaded v0.2.5 preview 6, can use accents in <help> RST
peterjc
parents: 20
diff changeset
170 Nielsen, Engelbrecht, Brunak and von Heijne (1997).
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
171 Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.
22
90e3d02f8013 Uploaded v0.2.5 preview 6, can use accents in <help> RST
peterjc
parents: 20
diff changeset
172 Protein Engineering, 10:1-6.
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
173 http://dx.doi.org/10.1093/protein/10.1.1
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
174
17
af3174637834 Uploaded v0.2.5 preview 1, adding links to Tool Shed entry
peterjc
parents: 7
diff changeset
175 This wrapper is available to install into other Galaxy Instances via the Galaxy
af3174637834 Uploaded v0.2.5 preview 1, adding links to Tool Shed entry
peterjc
parents: 7
diff changeset
176 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
177 </help>
25
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 22
diff changeset
178 <citations>
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 22
diff changeset
179 <citation type="doi">10.7717/peerj.167</citation>
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 22
diff changeset
180 <!-- TODO - select from these citations depending on method picked -->
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 22
diff changeset
181 <citation type="doi">10.1038/nature06203</citation>
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 22
diff changeset
182 <citation type="doi">10.1105/tpc.107.051037</citation>
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 22
diff changeset
183 <citation type="doi">10.1371/journal.ppat.0020050</citation>
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 22
diff changeset
184 <citation type="doi">10.1101/gr.910003</citation>
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 22
diff changeset
185 <citation type="doi">10.1093/bioinformatics/14.9.755</citation>
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 22
diff changeset
186 <citation type="doi">10.1093/protein/10.1.1</citation>
41a42022f815 Uploaded v0.2.6, embedded citations
peterjc
parents: 22
diff changeset
187 </citations>
6
39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
188 </tool>