Mercurial > repos > peterjc > tmhmm_and_signalp
comparison tools/protein_analysis/promoter2.xml @ 15:6abd809cefdd draft
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 |
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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. |