Mercurial > repos > peterjc > tmhmm_and_signalp

comparison tools/protein_analysis/signalp3.xml @ 9:e52220a9ddad draft

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Uploaded v0.1.2 Use the new <stdio> settings in the XML wrappers to catch errors. Obeys SGE style XNSLOTS environment variable for thread count (otherwise default to 4).
author peterjc
date Fri, 25 Jan 2013 06:08:31 -0500
parents 9b45a8743100
children 99b82a2b1272
comparison
equal deleted inserted replaced
8:976a5f2833cd 9:e52220a9ddad
1 <tool id="signalp3" name="SignalP 3.0" version="0.0.9"> 1 <tool id="signalp3" name="SignalP 3.0" version="0.0.10">
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 "\$NSLOTS" $fasta_file $tabular_file
8 ##Set the number of threads in the runner entry in universe_wsgi.ini 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. 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. 10 ##If the environment variable isn't set, get "", and defaults to one.
11 </command> 11 </command>
12 <stdio>
13 <!-- Anything other than zero is an error -->
14 <exit_code range="1:" />
15 <exit_code range=":-1" />
16 </stdio>
12 <inputs> 17 <inputs>
13 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> 18 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
14 <param name="organism" type="select" display="radio" label="Organism"> 19 <param name="organism" type="select" display="radio" label="Organism">
15 <option value="euk">Eukaryote</option> 20 <option value="euk">Eukaryote</option>
16 <option value="gram+">Gram positive</option> 21 <option value="gram+">Gram positive</option>