Mercurial > repos > peterjc > tmhmm_and_signalp

comparison tools/protein_analysis/promoter2.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="promoter2" name="Promoter 2.0" version="0.0.6"> 1 <tool id="promoter2" name="Promoter 2.0" version="0.0.8">
2 <description>Find eukaryotic PolII promoters in DNA sequences</description> 2 <description>Find eukaryotic PolII promoters in DNA 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 per chunk so 4 threads each doing 500 is ideal --> 4 <!-- Using 2000 per chunk so 4 threads each doing 500 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 promoter2.py "\$NSLOTS" $fasta_file $tabular_file 7 promoter2.py "\$GALAXY_SLOTS" "$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 -->
83 See also http://www.cbs.dtu.dk/services/Promoter/output.php 80 See also http://www.cbs.dtu.dk/services/Promoter/output.php
84 81
85 This wrapper is available to install into other Galaxy Instances via the Galaxy 82 This wrapper is available to install into other Galaxy Instances via the Galaxy
86 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp 83 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
87 </help> 84 </help>
85 <citations>
86 <citation type="doi">10.7717/peerj.167</citation>
87 <citation type="doi">10.1093/bioinformatics/15.5.356</citation>
88 </citations>
88 </tool> 89 </tool>