Mercurial > repos > peterjc > tmhmm_and_signalp
comparison tools/protein_analysis/signalp3.xml @ 7:5e62aefb2918 draft
Uploaded v0.1.2 to Test Tool Shed
| author | peterjc |
|---|---|
| date | Tue, 26 Mar 2013 14:24:56 -0400 |
| parents | 39a6e46cdda3 |
| children | 391a142c1e60 |
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| 6:39a6e46cdda3 | 7:5e62aefb2918 |
|---|---|
| 1 <tool id="signalp3" name="SignalP 3.0" version="0.0.8"> | 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 --> | |
| 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> |
| 12 <stdio> | |
| 13 <!-- Anything other than zero is an error --> | |
| 14 <exit_code range="1:" /> | |
| 15 <exit_code range=":-1" /> | |
| 16 </stdio> | |
| 7 <inputs> | 17 <inputs> |
| 8 <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"/> |
| 9 <param name="organism" type="select" display="radio" label="Organism"> | 19 <param name="organism" type="select" display="radio" label="Organism"> |
| 10 <option value="euk">Eukaryote</option> | 20 <option value="euk">Eukaryote</option> |
| 11 <option value="gram+">Gram positive</option> | 21 <option value="gram+">Gram positive</option> |