-
Notifications
You must be signed in to change notification settings - Fork 25
/
Copy pathwolf_psort.xml
150 lines (125 loc) · 6.05 KB
/
wolf_psort.xml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
<tool id="wolf_psort" name="WoLF PSORT" version="0.0.12">
<description>Eukaryote protein subcellular localization prediction</description>
<requirements>
<requirement type="package">wolfpsort</requirement>
</requirements>
<version_command>
python $__tool_directory__/wolf_psort.py --version
</version_command>
<command detect_errors="aggressive">
python $__tool_directory__/wolf_psort.py $organism "\$GALAXY_SLOTS" '$fasta_file' '$tabular_file'
</command>
<inputs>
<param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
<param name="organism" type="select" display="radio" label="Organism">
<option value="animal">Animal</option>
<option value="plant">Plant</option>
<option value="fungi">Fungi</option>
</param>
</inputs>
<outputs>
<data name="tabular_file" format="tabular" label="WoLF PSORT $organism results" />
</outputs>
<tests>
<test>
<param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta"/>
<param name="organism" value="animal"/>
<output name="tabular_file" file="four_human_proteins.wolf_psort.tabular" ftype="tabular"/>
</test>
<test>
<param name="fasta_file" value="empty.fasta" ftype="fasta"/>
<param name="organism" value="animal"/>
<output name="tabular_file" file="empty_wolf_psort.tabular" ftype="tabular"/>
</test>
<test>
<param name="fasta_file" value="empty.fasta" ftype="fasta"/>
<param name="organism" value="plant"/>
<output name="tabular_file" file="empty_wolf_psort.tabular" ftype="tabular"/>
</test>
<test>
<param name="fasta_file" value="empty.fasta" ftype="fasta"/>
<param name="organism" value="fungi"/>
<output name="tabular_file" file="empty_wolf_psort.tabular" ftype="tabular"/>
</test>
</tests>
<help>
**What it does**
This calls the WoLF PSORT tool for prediction of eukaryote protein subcellular localization.
The input is a FASTA file of protein sequences, and the output is tabular with four columns (multiple rows per protein):
====== ===================
Column Description
------ -------------------
1 Sequence identifier
2 Compartment
3 Score
4 Prediction rank
====== ===================
**Localization Compartments**
The table below gives the WoLF PSORT localization site definitions, and the corresponding Gene Ontology (GO) term.
====== ===================== =====================
Abbrev Localization Site GO Cellular Component
------ --------------------- ---------------------
chlo chloroplast 0009507, 0009543
cyto cytosol 0005829
cysk cytoskeleton 0005856(2)
E.R. endoplasmic reticulum 0005783
extr extracellular 0005576, 0005618
golg Golgi apparatus 0005794(1)
lyso lysosome 0005764
mito mitochondria 0005739
nucl nuclear 0005634
pero peroxisome 0005777(2)
plas plasma membrane 0005886
vacu vacuolar membrane 0005774(2)
====== ===================== =====================
Numbers in parentheses, such as "0005856(2)" indicate that descendant "part_of"
cellular components were also included, up to the specified depth (2 in this case).
For example, all of the children and grandchildren of "GO:0005856" were
included as "cysk".
Additionally compound predictions like mito_nucl are also given.
**Notes**
The raw output from WoLF PSORT looks like this (space separated), showing two proteins:
================================ ============================================
gi|301087619|ref|XP_002894699.1| extr 12, mito 4, E.R. 3, golg 3, mito_nucl 3
gi|301087623|ref|XP_002894700.1| extr 21, mito 2, cyto 2, cyto_mito 2
================================ ============================================
This is reformatted into a tabular file as follows for use in Galaxy:
================================ =========== ===== ====
#ID Compartment Score Rank
-------------------------------- ----------- ----- ----
gi|301087619|ref|XP_002894699.1| extr 12 1
gi|301087619|ref|XP_002894699.1| mito 4 2
gi|301087619|ref|XP_002894699.1| E.R. 3 3
gi|301087619|ref|XP_002894699.1| golg 3 4
gi|301087619|ref|XP_002894699.1| mito_nucl 3 5
gi|301087623|ref|XP_002894700.1| extr 21 1
gi|301087623|ref|XP_002894700.1| mito 2 2
gi|301087623|ref|XP_002894700.1| cyto 2 3
gi|301087623|ref|XP_002894700.1| cyto_mito 2 4
================================ =========== ===== ====
This way you can easily filter for things like having a top prediction for
mitochondria (c2=='mito' and c4==1), or extracellular with a score of at
least 10 (c2=='extr' and 10<=c3), and so on.
**References**
If you use this Galaxy tool in work leading to a scientific publication please
cite the following papers:
Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
Galaxy tools and workflows for sequence analysis with applications
in molecular plant pathology. PeerJ 1:e167
https://doi.org/10.7717/peerj.167
Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C.J. Adams-Collier, and Kenta Nakai (2007).
WoLF PSORT: Protein Localization Predictor.
Nucleic Acids Research, 35(S2), W585-W587.
https://doi.org/10.1093/nar/gkm259
Paul Horton, Keun-Joon Park, Takeshi Obayashi and Kenta Nakai (2006).
Protein Subcellular Localization Prediction with WoLF PSORT.
Proceedings of the 4th Annual Asia Pacific Bioinformatics Conference APBC06, Taipei, Taiwan. pp. 39-48.
See also http://wolfpsort.org
This wrapper is available to install into other Galaxy Instances via the Galaxy
Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
</help>
<citations>
<citation type="doi">10.7717/peerj.167</citation>
<citation type="doi">10.1093/nar/gkm259</citation>
</citations>
</tool>