Mercurial > repos > peterjc > tmhmm_and_signalp

comparison tools/protein_analysis/tmhmm2.xml @ 25:41a42022f815 draft

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Uploaded v0.2.6, embedded citations
author peterjc
date Fri, 21 Nov 2014 08:17:36 -0500
parents 90e3d02f8013
children 20139cb4c844
comparison
equal deleted inserted replaced
24:ee10017fcd80 25:41a42022f815
1 <tool id="tmhmm2" name="TMHMM 2.0" version="0.0.11"> 1 <tool id="tmhmm2" name="TMHMM 2.0" version="0.0.13">
2 <description>Find transmembrane domains in protein sequences</description> 2 <description>Find transmembrane domains in protein sequences</description>
3 <!-- If job splitting is enabled, break up the query file into parts --> 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 --> 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> 5 <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
6 <command interpreter="python"> 6 <command interpreter="python">
7 tmhmm2.py "\$NSLOTS" $fasta_file $tabular_file 7 tmhmm2.py "\$GALAXY_SLOTS" $fasta_file $tabular_file
8 ##I want the number of threads to be a Galaxy config option...
9 ##Set the number of threads in the runner entry in universe_wsgi.ini
10 ##which (on SGE at least) will set the $NSLOTS environment variable.
11 ##If the environment variable isn't set, get "", and the python wrapper 8 ##If the environment variable isn't set, get "", and the python wrapper
12 ##defaults to four threads. 9 ##defaults to four threads.
13 </command> 10 </command>
14 <stdio> 11 <stdio>
15 <!-- Anything other than zero is an error --> 12 <!-- Anything other than zero is an error -->
117 See also http://www.cbs.dtu.dk/services/TMHMM/ 114 See also http://www.cbs.dtu.dk/services/TMHMM/
118 115
119 This wrapper is available to install into other Galaxy Instances via the Galaxy 116 This wrapper is available to install into other Galaxy Instances via the Galaxy
120 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp 117 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
121 </help> 118 </help>
119 <citations>
120 <citation type="doi">10.7717/peerj.167</citation>
121 <citation type="doi">10.1006/jmbi.2000.4315</citation>
122 <!-- TODO - add entry for PMID: 9783223 -->
123 </citations>
122 </tool> 124 </tool>