comparison tools/protein_analysis/promoter2.xml @ 8:976a5f2833cd draft

Uploaded v0.1.1 of the bundle, which fixes an error in the header of the tabular output produced for Promoter 2.0

7:9b45a8743100

<tool id="promoter2" name="Promoter 2.0" version="0.0.1">
    <description>Find eukaryotic PolII promoters in DNA sequences</description>
    <!-- If job splitting is enabled, break up the query file into parts -->
    <!-- Using 2000 per chunk so 4 threads each doing 500 is ideal -->
    <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
    <command interpreter="python">

    </requirements>
    <help>
    
**What it does**

This calls the Promoter 2.0 tool for prediction of eukaryotic PolII promoters sequences using a Neural Network (NN) model.

The input is a FASTA file of nucleotide sequences (e.g. upstream regions of your genes), and the output is tabular with five columns (one row per promoter):

 1. Sequence identifier (first word of FASTA header)
 2. Promoter position, e.g. 600

8:976a5f2833cd

<tool id="promoter2" name="Promoter 2.0" version="0.0.2">
    <description>Find eukaryotic PolII promoters in DNA sequences</description>
    <!-- If job splitting is enabled, break up the query file into parts -->
    <!-- Using 2000 per chunk so 4 threads each doing 500 is ideal -->
    <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
    <command interpreter="python">

    </requirements>
    <help>
    
**What it does**

This calls the Promoter 2.0 tool for prediction of eukaryotic PolII promoter sequences using a Neural Network (NN) model.

The input is a FASTA file of nucleotide sequences (e.g. upstream regions of your genes), and the output is tabular with five columns (one row per promoter):

 1. Sequence identifier (first word of FASTA header)
 2. Promoter position, e.g. 600