comparison tools/protein_analysis/tmhmm2.xml @ 17:e6cc27d182a8 draft

Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS

16:7de64c8b258d

<tool id="tmhmm2" name="TMHMM 2.0" version="0.0.11">
    <description>Find transmembrane domains in 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>
    <command interpreter="python">
      tmhmm2.py "\$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 the python wrapper
      ##defaults to four threads.
    </command>
    <stdio>
        <!-- Anything other than zero is an error -->

See also http://www.cbs.dtu.dk/services/TMHMM/

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="tmhmm2" name="TMHMM 2.0" version="0.0.13">
    <description>Find transmembrane domains in 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>
    <command interpreter="python">
      tmhmm2.py "\$GALAXY_SLOTS" $fasta_file $tabular_file
      ##If the environment variable isn't set, get "", and the python wrapper
      ##defaults to four threads.
    </command>
    <stdio>
        <!-- Anything other than zero is an error -->

See also http://www.cbs.dtu.dk/services/TMHMM/

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>
    <citations>
        <citation type="doi">10.7717/peerj.167</citation>
        <citation type="doi">10.1006/jmbi.2000.4315</citation>
        <!-- TODO - add entry for PMID: 9783223 -->
    </citations>
</tool>