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comparison tools/protein_analysis/signalp3.xml @ 18:eb6ac44d4b8e draft

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Suite v0.2.8, record Promoter 2 verion + misc internal updates
author peterjc
date Tue, 01 Sep 2015 09:56:36 -0400
parents e6cc27d182a8
children a19b3ded8f33
comparison
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17:e6cc27d182a8 18:eb6ac44d4b8e
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"/>