Mercurial > repos > peterjc > tmhmm_and_signalp
diff tools/protein_analysis/tmhmm2.xml @ 25:41a42022f815 draft
Uploaded v0.2.6, embedded citations
author | peterjc |
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date | Fri, 21 Nov 2014 08:17:36 -0500 |
parents | 90e3d02f8013 |
children | 20139cb4c844 |
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--- a/tools/protein_analysis/tmhmm2.xml Tue Sep 17 12:06:15 2013 -0400 +++ b/tools/protein_analysis/tmhmm2.xml Fri Nov 21 08:17:36 2014 -0500 @@ -1,13 +1,10 @@ -<tool id="tmhmm2" name="TMHMM 2.0" version="0.0.11"> +<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 "\$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. + 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> @@ -119,4 +116,9 @@ 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>