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comparison tools/protein_analysis/promoter2.xml @ 15:6abd809cefdd draft

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Uploaded v0.2.4, added unit tests for Promoter 2
author peterjc
date Thu, 25 Apr 2013 12:25:52 -0400
parents e52220a9ddad
children 7de64c8b258d
comparison
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14:6365217cd3de 15:6abd809cefdd
1 <tool id="promoter2" name="Promoter 2.0" version="0.0.3"> 1 <tool id="promoter2" name="Promoter 2.0" version="0.0.4">
2 <description>Find eukaryotic PolII promoters in DNA sequences</description> 2 <description>Find eukaryotic PolII promoters in DNA 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 per chunk so 4 threads each doing 500 is ideal --> 4 <!-- Using 2000 per chunk so 4 threads each doing 500 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">
21 <data name="tabular_file" format="tabular" label="Promoter2 on ${fasta_file.name}" /> 21 <data name="tabular_file" format="tabular" label="Promoter2 on ${fasta_file.name}" />
22 </outputs> 22 </outputs>
23 <requirements> 23 <requirements>
24 <requirement type="binary">promoter</requirement> 24 <requirement type="binary">promoter</requirement>
25 </requirements> 25 </requirements>
26 <tests>
27 <test>
28 <param name="fasta_file" value="Adenovirus.fasta" ftype="fasta"/>
29 <output name="tabular_file" file="Adenovirus.promoter2.tabular" ftype="tabular"/>
30 </test>
31 <test>
32 <param name="fasta_file" value="empty.fasta" ftype="fasta"/>
33 <output name="tabular_file" file="empty_promoter2.tabular" ftype="tabular"/>
34 </test>
35 </tests>
26 <help> 36 <help>
27 37
28 **What it does** 38 **What it does**
29 39
30 This calls the Promoter 2.0 tool for prediction of eukaryotic PolII promoter sequences using a Neural Network (NN) model. 40 This calls the Promoter 2.0 tool for prediction of eukaryotic PolII promoter sequences using a Neural Network (NN) model.