comparison tools/protein_analysis/psortb.xml @ 17:e6cc27d182a8 draft

Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS

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>
  <inputs>
    <param format="fasta" name="sequence" type="data"
	   label="Input sequences for which to predict localisation (protein FASTA format)" />
    <param name="type" type="select"
	   label="Organism type (N.B. all sequences in the above file must be of the same type)" >
      <option value="-p">Gram positive bacteria</option>
      <option value="-n">Gram negative bacteria</option>
      <option value="-a">Archaea</option>
    </param>
    <param name="long" type="select" label="Output type">

      <option value="normal">Normal</option>
      -->
      <option value="long">Long (verbose, tabular with about 30 columns, depending on organism type)</option>
    </param>
    <param name="cutoff" size="10" type="float" optional="true" value=""
	   label="Sets a cutoff value for reported results (e.g. 7.5)"
	   help="Leave blank or use zero for no cutoff." />
    <param name="divergent" size="10" type="float" optional="true" value=""
	   label="Sets a cutoff value for the multiple localization flag (e.g. 4.5)"
	   help="Leave blank or use zero for no cutoff." />
  </inputs>
  <outputs>
    <data format="tabular" name="outfile" />
  </outputs>
  <requirements>

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>

17:e6cc27d182a8

<tool id="Psortb" name="psortb" version="0.0.5">
  <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 "\$GALAXY_SLOTS" "$type" "$long" "$cutoff" "$divergent" "$sequence" "$outfile"
    ##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>
  <inputs>
    <param format="fasta" name="sequence" type="data"
           label="Input sequences for which to predict localisation (protein FASTA format)" />
    <param name="type" type="select"
           label="Organism type (N.B. all sequences in the above file must be of the same type)" >
      <option value="-p">Gram positive bacteria</option>
      <option value="-n">Gram negative bacteria</option>
      <option value="-a">Archaea</option>
    </param>
    <param name="long" type="select" label="Output type">

      <option value="normal">Normal</option>
      -->
      <option value="long">Long (verbose, tabular with about 30 columns, depending on organism type)</option>
    </param>
    <param name="cutoff" size="10" type="float" optional="true" value=""
           label="Sets a cutoff value for reported results (e.g. 7.5)"
           help="Leave blank or use zero for no cutoff." />
    <param name="divergent" size="10" type="float" optional="true" value=""
           label="Sets a cutoff value for the multiple localization flag (e.g. 4.5)"
           help="Leave blank or use zero for no cutoff." />
  </inputs>
  <outputs>
    <data format="tabular" name="outfile" />
  </outputs>
  <requirements>

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
    <citations>
        <citation type="doi">10.7717/peerj.167</citation>
        <citation type="doi">10.1093/bioinformatics/btq249</citation>
    </citations>
  </help>
</tool>