Mercurial > repos > peterjc > tmhmm_and_signalp
comparison tools/protein_analysis/signalp3.xml @ 26:20139cb4c844 draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty
| author | peterjc |
|---|---|
| date | Wed, 13 May 2015 06:14:42 -0400 |
| parents | 41a42022f815 |
| children | 6d9d7cdf00fc |
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| 25:41a42022f815 | 26:20139cb4c844 |
|---|---|
| 1 <tool id="signalp3" name="SignalP 3.0" version="0.0.14"> | 1 <tool id="signalp3" name="SignalP 3.0" version="0.0.15"> |
| 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 <requirements> | |
| 7 <requirement type="binary">signalp</requirement> | |
| 8 <requirement type="package">signalp</requirement> | |
| 9 </requirements> | |
| 10 <stdio> | |
| 11 <!-- Anything other than zero is an error --> | |
| 12 <exit_code range="1:" /> | |
| 13 <exit_code range=":-1" /> | |
| 14 </stdio> | |
| 6 <command interpreter="python"> | 15 <command interpreter="python"> |
| 7 signalp3.py $organism $truncate "\$GALAXY_SLOTS" $fasta_file $tabular_file | 16 signalp3.py $organism $truncate "\$GALAXY_SLOTS" $fasta_file $tabular_file |
| 8 ##If the environment variable isn't set, get "", and the python wrapper | 17 ##If the environment variable isn't set, get "", and the python wrapper |
| 9 ##defaults to four threads. | 18 ##defaults to four threads. |
| 10 </command> | 19 </command> |
| 11 <stdio> | |
| 12 <!-- Anything other than zero is an error --> | |
| 13 <exit_code range="1:" /> | |
| 14 <exit_code range=":-1" /> | |
| 15 </stdio> | |
| 16 <inputs> | 20 <inputs> |
| 17 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> | 21 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> |
| 18 <param name="organism" type="select" display="radio" label="Organism"> | 22 <param name="organism" type="select" display="radio" label="Organism"> |
| 19 <option value="euk">Eukaryote</option> | 23 <option value="euk">Eukaryote</option> |
| 20 <option value="gram+">Gram positive</option> | 24 <option value="gram+">Gram positive</option> |
| 25 </param> | 29 </param> |
| 26 </inputs> | 30 </inputs> |
| 27 <outputs> | 31 <outputs> |
| 28 <data name="tabular_file" format="tabular" label="SignalP $organism results" /> | 32 <data name="tabular_file" format="tabular" label="SignalP $organism results" /> |
| 29 </outputs> | 33 </outputs> |
| 30 <requirements> | |
| 31 <requirement type="binary">signalp</requirement> | |
| 32 </requirements> | |
| 33 <tests> | 34 <tests> |
| 34 <test> | 35 <test> |
| 35 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta"/> | 36 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta"/> |
| 36 <param name="organism" value="euk"/> | 37 <param name="organism" value="euk"/> |
| 37 <param name="truncate" value="0"/> | 38 <param name="truncate" value="0"/> |