comparison tools/protein_analysis/wolf_psort.xml @ 16:7de64c8b258d draft

Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub

15:6abd809cefdd

<tool id="wolf_psort" name="WoLF PSORT" version="0.0.4">
    <description>Eukaryote protein subcellular localization prediction</description>
    <command interpreter="python">
      wolf_psort.py $organism 8 $fasta_file $tabular_file
      ##I want the number of threads to be a Galaxy config option...
    </command>
    <stdio>
        <!-- Anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />

pero   peroxisome	     0005777(2)
plas   plasma membrane	     0005886
vacu   vacuolar membrane     0005774(2)
====== ===================== =====================

Additionally compound predictions like mito_nucl are also given.


**Notes**

least 10 (c2=='extr' and 10<=c3), and so on.


**References**

Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C.J. Adams-Collier, and Kenta Nakai,
WoLF PSORT: Protein Localization Predictor.
Nucleic Acids Research, 35(S2), W585-W587, 2007.
http://dx.doi.org/10.1093/nar/gkm259

Paul Horton, Keun-Joon Park, Takeshi Obayashi and Kenta Nakai.
Protein Subcellular Localization Prediction with WoLF PSORT.
Proceedings of the 4th Annual Asia Pacific Bioinformatics Conference APBC06, Taipei, Taiwan. pp. 39-48, 2006.

http://wolfpsort.org

    </help>
</tool>

16:7de64c8b258d

<tool id="wolf_psort" name="WoLF PSORT" version="0.0.6">
    <description>Eukaryote protein subcellular localization prediction</description>
    <command interpreter="python">
      wolf_psort.py $organism "\$NSLOTS" "$fasta_file" "$tabular_file"
      ##I want the number of threads to be a Galaxy config option...
      ##Set the number of threads in the runner entry in universe_wsgi.ini
      ##which (on SGE at least) will set the $NSLOTS environment variable.
      ##If the environment variable isn't set, get "", and python wrapper
      ##defaults to four threads.
    </command>
    <stdio>
        <!-- Anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />

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**

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
http://dx.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.
http://dx.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>
</tool>