Mercurial > repos > peterjc > tmhmm_and_signalp

comparison tools/protein_analysis/signalp3.xml @ 17:e6cc27d182a8 draft

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Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
author peterjc
date Fri, 21 Nov 2014 08:19:09 -0500
parents 7de64c8b258d
children eb6ac44d4b8e
comparison
equal deleted inserted replaced
16:7de64c8b258d 17:e6cc27d182a8
1 <tool id="signalp3" name="SignalP 3.0" version="0.0.12"> 1 <tool id="signalp3" name="SignalP 3.0" version="0.0.14">
2 <description>Find signal peptides in protein sequences</description> 2 <description>Find signal peptides 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 signalp3.py $organism $truncate "\$NSLOTS" $fasta_file $tabular_file 7 signalp3.py $organism $truncate "\$GALAXY_SLOTS" $fasta_file $tabular_file
8 ##Set the number of threads in the runner entry in universe_wsgi.ini
9 ##which (on SGE at least) will set the $NSLOTS environment variable.
10 ##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
11 ##defaults to four threads. 9 ##defaults to four threads.
12 </command> 10 </command>
13 <stdio> 11 <stdio>
14 <!-- Anything other than zero is an error --> 12 <!-- Anything other than zero is an error -->
195 See also http://www.cbs.dtu.dk/services/SignalP-3.0/output.php 193 See also http://www.cbs.dtu.dk/services/SignalP-3.0/output.php
196 194
197 This wrapper is available to install into other Galaxy Instances via the Galaxy 195 This wrapper is available to install into other Galaxy Instances via the Galaxy
198 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp 196 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
199 </help> 197 </help>
198 <citations>
199 <citation type="doi">10.7717/peerj.167</citation>
200 <citation type="doi">10.1016/j.jmb.2004.05.028</citation>
201 <citation type="doi">10.1093/protein/10.1.1</citation>
202 <!-- TODO - Add bibtex entry for PMID: 9783217 -->
203 </citations>
200 </tool> 204 </tool>