Mercurial > repos > peterjc > tmhmm_and_signalp
comparison tools/protein_analysis/signalp3.xml @ 7:9b45a8743100 draft
Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers.
author | peterjc |
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date | Mon, 30 Jul 2012 10:25:07 -0400 |
parents | a290c6d4e658 |
children | e52220a9ddad |
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6:a290c6d4e658 | 7:9b45a8743100 |
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1 <tool id="signalp3" name="SignalP 3.0" version="0.0.8"> | 1 <tool id="signalp3" name="SignalP 3.0" version="0.0.9"> |
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 --> | |
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> | |
3 <command interpreter="python"> | 6 <command interpreter="python"> |
4 signalp3.py $organism $truncate 8 $fasta_file $tabular_file | 7 signalp3.py $organism $truncate "\$NSLOTS" $fasta_file $tabular_file |
5 ##I want the number of threads to be a Galaxy config option... | 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 defaults to one. | |
6 </command> | 11 </command> |
7 <inputs> | 12 <inputs> |
8 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> | 13 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> |
9 <param name="organism" type="select" display="radio" label="Organism"> | 14 <param name="organism" type="select" display="radio" label="Organism"> |
10 <option value="euk">Eukaryote</option> | 15 <option value="euk">Eukaryote</option> |