|
8
|
1 <tool id="Psortb" name="psortb" version="0.0.1">
|
|
|
2 <description>Determines sub-cellular localisation of bacterial/archaeal protein sequences</description>
|
|
|
3 <!-- If job splitting is enabled, break up the query file into parts -->
|
|
|
4 <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal -->
|
|
|
5 <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
|
|
|
6 <version_command interpreter="python">psortb.py --version</version_command>
|
|
|
7 <command interpreter="python">psortb.py "\$NSLOTS" "$type" "$long" "$cutoff" "$divergent" "$sequence" "$outfile"</command>
|
|
|
8 <stdio>
|
|
|
9 <!-- Anything other than zero is an error -->
|
|
|
10 <exit_code range="1:" />
|
|
|
11 <exit_code range=":-1" />
|
|
|
12 </stdio>
|
|
|
13 <inputs>
|
|
|
14 <param format="fasta" name="sequence" type="data"
|
|
|
15 label="Input sequences for which to predict localisation (protein FASTA format)" />
|
|
|
16 <param name="type" type="select"
|
|
|
17 label="Organism type (N.B. all sequences in the above file must be of the same type)" >
|
|
|
18 <option value="-p">Gram positive bacteria</option>
|
|
|
19 <option value="-n">Gram negative bacteria</option>
|
|
|
20 <option value="-a">Archaea</option>
|
|
|
21 </param>
|
|
|
22 <param name="long" type="select" label="Output type">
|
|
|
23 <option value="terse">Short (terse, tabular with 3 columns)</option>
|
|
|
24 <!-- The normal output is text, not tabular - worth offering?
|
|
|
25 <option value="normal">Normal</option>
|
|
|
26 -->
|
|
|
27 <option value="long">Long (verbose, tabular with about 30 columns, depending on organism type)</option>
|
|
|
28 </param>
|
|
|
29 <param name="cutoff" size="10" type="float" optional="true" value=""
|
|
|
30 label="Sets a cutoff value for reported results (e.g. 7.5)"
|
|
|
31 help="Leave blank or use zero for no cutoff." />
|
|
|
32 <param name="divergent" size="10" type="float" optional="true" value=""
|
|
|
33 label="Sets a cutoff value for the multiple localization flag (e.g. 4.5)"
|
|
|
34 help="Leave blank or use zero for no cutoff." />
|
|
|
35 </inputs>
|
|
|
36 <outputs>
|
|
|
37 <data format="tabular" name="outfile" />
|
|
|
38 </outputs>
|
|
|
39 <requirements>
|
|
|
40 <requirement type="binary">psort</requirement>
|
|
|
41 </requirements>
|
|
|
42 <tests>
|
|
|
43 <test>
|
|
11
|
44 <param name="sequence" value="empty.fasta" ftype="fasta"/>
|
|
|
45 <param name="long" value="terse"/>
|
|
|
46 <output name="outfile" file="empty_psortb_terse.tabular" ftype="tabular"/>
|
|
|
47 </test>
|
|
|
48 <test>
|
|
8
|
49 <param name="sequence" value="k12_ten_proteins.fasta" ftype="fasta"/>
|
|
|
50 <param name="long" value="terse"/>
|
|
|
51 <output name="outfile" file="k12_ten_proteins_psortb_p_terse.tabular" ftype="tabular"/>
|
|
|
52 </test>
|
|
|
53 </tests>
|
|
|
54 <help>
|
|
|
55
|
|
|
56 **What it does**
|
|
|
57
|
|
|
58 This calls the command line tool PSORTb v3.0 for prediction of prokaryotic
|
|
|
59 localization sites. The input dataset needs to be protein FASTA sequences.
|
|
|
60 The default output is a simple tabular file with three columns, one row
|
|
|
61 per query sequence:
|
|
|
62
|
|
|
63 ====== ==============================
|
|
|
64 Column Description
|
|
|
65 ------ ------------------------------
|
|
|
66 1 Sequence identifier
|
|
|
67 2 Localisation, e.g. Cytoplasmic
|
|
|
68 3 Score
|
|
|
69 ====== ==============================
|
|
|
70
|
|
|
71 The long output is also tabular with one row per query sequence, but has
|
|
|
72 lots more columns (a different set for each supported organism type). In
|
|
|
73 both cases, a simple header line is included (starting with a hash, #,
|
|
|
74 so that Galaxy treats it as a comment) giving the column names.
|
|
|
75
|
|
|
76
|
|
|
77 **References**
|
|
|
78
|
|
|
79 N.Y. Yu, J.R. Wagner, M.R. Laird, G. Melli, S. Rey, R. Lo, P. Dao,
|
|
|
80 S.C. Sahinalp, M. Ester, L.J. Foster, F.S.L. Brinkman (2010)
|
|
|
81 PSORTb 3.0: Improved protein subcellular localization prediction with
|
|
|
82 refined localization subcategories and predictive capabilities for all
|
|
|
83 prokaryotes, Bioinformatics 26(13):1608-1615
|
|
|
84 http://dx.doi.org/10.1093/bioinformatics/btq249
|
|
|
85
|
|
|
86 http://www.psort.org/documentation/index.html
|
|
|
87
|
|
|
88 </help>
|
|
|
89 </tool>
|
