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comparison tools/protein_analysis/psortb.xml @ 8:391a142c1e60 draft

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author peterjc
date Tue, 26 Mar 2013 14:27:44 -0400
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7:5e62aefb2918 8:391a142c1e60
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>
44 <param name="sequence" value="k12_ten_proteins.fasta" ftype="fasta"/>
45 <param name="long" value="terse"/>
46 <output name="outfile" file="k12_ten_proteins_psortb_p_terse.tabular" ftype="tabular"/>
47 </test>
48 </tests>
49 <help>
50
51 **What it does**
52
53 This calls the command line tool PSORTb v3.0 for prediction of prokaryotic
54 localization sites. The input dataset needs to be protein FASTA sequences.
55 The default output is a simple tabular file with three columns, one row
56 per query sequence:
57
58 ====== ==============================
59 Column Description
60 ------ ------------------------------
61 1 Sequence identifier
62 2 Localisation, e.g. Cytoplasmic
63 3 Score
64 ====== ==============================
65
66 The long output is also tabular with one row per query sequence, but has
67 lots more columns (a different set for each supported organism type). In
68 both cases, a simple header line is included (starting with a hash, #,
69 so that Galaxy treats it as a comment) giving the column names.
70
71
72 **References**
73
74 N.Y. Yu, J.R. Wagner, M.R. Laird, G. Melli, S. Rey, R. Lo, P. Dao,
75 S.C. Sahinalp, M. Ester, L.J. Foster, F.S.L. Brinkman (2010)
76 PSORTb 3.0: Improved protein subcellular localization prediction with
77 refined localization subcategories and predictive capabilities for all
78 prokaryotes, Bioinformatics 26(13):1608-1615
79 http://dx.doi.org/10.1093/bioinformatics/btq249
80
81 http://www.psort.org/documentation/index.html
82
83 </help>
84 </tool>