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

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

15:6abd809cefdd

<tool id="Psortb" name="psortb" version="0.0.1">
  <description>Determines sub-cellular localisation of bacterial/archaeal protein sequences</description>
  <!-- If job splitting is enabled, break up the query file into parts -->
  <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal -->
  <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
  <version_command interpreter="python">psortb.py --version</version_command>
  <command interpreter="python">psortb.py "\$NSLOTS" "$type" "$long" "$cutoff" "$divergent" "$sequence" "$outfile"</command>
  <stdio>
    <!-- Anything other than zero is an error -->
    <exit_code range="1:" />
    <exit_code range=":-1" />
  </stdio>

so that Galaxy treats it as a comment) giving the column names.


**References**

N.Y. Yu, J.R. Wagner, M.R. Laird, G. Melli, S. Rey, R. Lo, P. Dao,
S.C. Sahinalp, M. Ester, L.J. Foster, F.S.L. Brinkman (2010)
PSORTb 3.0: Improved protein subcellular localization prediction with
refined localization subcategories and predictive capabilities for all
prokaryotes, Bioinformatics 26(13):1608-1615
http://dx.doi.org/10.1093/bioinformatics/btq249

http://www.psort.org/documentation/index.html

  </help>
</tool>

16:7de64c8b258d

<tool id="Psortb" name="psortb" version="0.0.3">
  <description>Determines sub-cellular localisation of bacterial/archaeal protein sequences</description>
  <!-- If job splitting is enabled, break up the query file into parts -->
  <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal -->
  <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
  <version_command interpreter="python">psortb.py --version</version_command>
  <command interpreter="python">
    psortb.py "\$NSLOTS" "$type" "$long" "$cutoff" "$divergent" "$sequence" "$outfile"
    ##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" />
  </stdio>

so that Galaxy treats it as a comment) giving the column names.


**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

N.Y. Yu, J.R. Wagner, M.R. Laird, G. Melli, S. Rey, R. Lo, P. Dao,
S.C. Sahinalp, M. Ester, L.J. Foster, F.S.L. Brinkman (2010)
PSORTb 3.0: Improved protein subcellular localization prediction with
refined localization subcategories and predictive capabilities for all
prokaryotes, Bioinformatics 26(13):1608-1615
http://dx.doi.org/10.1093/bioinformatics/btq249

See also http://www.psort.org/documentation/index.html

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>