Mercurial > repos > peterjc > tmhmm_and_signalp

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

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Uploaded v0.1.1 of the bundle, which fixes an error in the header of the tabular output produced for Promoter 2.0
author peterjc
date Mon, 30 Jul 2012 12:56:54 -0400
parents 9b45a8743100
children e52220a9ddad
comparison
equal deleted inserted replaced
7:9b45a8743100 8:976a5f2833cd
1 <tool id="promoter2" name="Promoter 2.0" version="0.0.1"> 1 <tool id="promoter2" name="Promoter 2.0" version="0.0.2">
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">
20 </requirements> 20 </requirements>
21 <help> 21 <help>
22 22
23 **What it does** 23 **What it does**
24 24
25 This calls the Promoter 2.0 tool for prediction of eukaryotic PolII promoters sequences using a Neural Network (NN) model. 25 This calls the Promoter 2.0 tool for prediction of eukaryotic PolII promoter sequences using a Neural Network (NN) model.
26 26
27 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): 27 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):
28 28
29 1. Sequence identifier (first word of FASTA header) 29 1. Sequence identifier (first word of FASTA header)
30 2. Promoter position, e.g. 600 30 2. Promoter position, e.g. 600