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comparison tools/protein_analysis/promoter2.xml @ 19:4cd848c5590b draft

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Uploaded v0.2.5 preview 3, use $NSLOTS in the PSORT wrappers.
author peterjc
date Thu, 23 May 2013 12:49:18 -0400
parents af3174637834
children a538e182fab3
comparison
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18:2b35b5c4b7f4 19:4cd848c5590b
1 <tool id="promoter2" name="Promoter 2.0" version="0.0.5"> 1 <tool id="promoter2" name="Promoter 2.0" version="0.0.6">
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">
7 promoter2.py "\$NSLOTS" $fasta_file $tabular_file 7 promoter2.py "\$NSLOTS" $fasta_file $tabular_file
8 ##I want the number of threads to be a Galaxy config option...
8 ##Set the number of threads in the runner entry in universe_wsgi.ini 9 ##Set the number of threads in the runner entry in universe_wsgi.ini
9 ##which (on SGE at least) will set the $NSLOTS environment variable. 10 ##which (on SGE at least) will set the $NSLOTS environment variable.
10 ##If the environment variable isn't set, get "", and defaults to one. 11 ##If the environment variable isn't set, get "", and the python wrapper
12 ##defaults to four threads.
11 </command> 13 </command>
12 <stdio> 14 <stdio>
13 <!-- Anything other than zero is an error --> 15 <!-- Anything other than zero is an error -->
14 <exit_code range="1:" /> 16 <exit_code range="1:" />
15 <exit_code range=":-1" /> 17 <exit_code range=":-1" />
39 41
40 This calls the Promoter 2.0 tool for prediction of eukaryotic PolII promoter sequences using a Neural Network (NN) model. 42 This calls the Promoter 2.0 tool for prediction of eukaryotic PolII promoter sequences using a Neural Network (NN) model.
41 43
42 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): 44 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):
43 45
44 1. Sequence identifier (first word of FASTA header) 46 ====== ==================================================
45 2. Promoter position, e.g. 600 47 Column Description
46 3. Promoter score, e.g. 1.063 48 ------ --------------------------------------------------
47 4. Promoter likelihood, e.g. Highly likely prediction 49 1 Sequence identifier (first word of FASTA header)
50 2 Promoter position, e.g. 600
51 3 Promoter score, e.g. 1.063
52 4 Promoter likelihood, e.g. Highly likely prediction
53 ====== ==================================================
48 54
49 The scores are classified very simply as follows: 55 The scores are classified very simply as follows:
50 56
51 ========= ======================== 57 ========= ========================
52 Score Description 58 Score Description