Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/tmhmm2.xml @ 0:a2eeeaa6f75e

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 17:37:26 -0400
parents
children 9a8a7f680dd6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
1 <tool id="tmhmm2" name="TMHMM 2.0" version="0.0.1">
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
2 <description>Find transmembrane domains in protein sequences</description>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
3 <command interpreter="python">
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
4 tmhmm2.py 8 $fasta_file $tabular_file
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
5 ##I want the number of threads to be a Galaxy config option...
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
6 </command>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
7 <inputs>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
8 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
9 <!--
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
10 <param name="version" type="select" display="radio" label="Model version">
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
11 <option value="">Version 1 (old)</option>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
12 <option value="" selected="True">Version 2 (default)</option>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
13 </param>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
14 -->
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
15 </inputs>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
16 <outputs>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
17 <data name="tabular_file" format="tabular" label="TMHMM results" />
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
18 </outputs>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
19 <requirements>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
20 <requirement type="binary">tmhmm</requirement>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
21 </requirements>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
22 <tests>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
23 <test>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
24 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta"/>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
25 <output name="tabular_file" file="four_human_proteins.tmhmm2.tsv" ftype="tabular"/>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
26 </test>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
27 </tests>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
28 <help>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
29
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
30 **What it does**
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
31
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
32 This calls the TMHMM v2.0 tool for prediction of transmembrane (TM) helices in proteins using a hidden Markov model (HMM).
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
33
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
34 The input is a FASTA file of protein sequences, and the output is tabular with six columns (one row per protein):
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
35
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
36 1. Sequence identifier
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
37 2. Sequence length
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
38 3. Expected number of amino acids in TM helices (ExpAA). If this number is larger than 18 it is very likely to be a transmembrane protein (OR have a signal peptide).
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
39 4. Expected number of amino acids in TM helices in the first 60 amino acids of the protein (Exp60). If this number more than a few, be aware that a predicted transmembrane helix in the N-term could be a signal peptide.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
40 5. Number of transmembrane helices predicted by N-best.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
41 6. Topology predicted by N-best (encoded as a strip using o for output and i for inside)
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
42
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
43 Predicted TM segments in the n-terminal region sometime turn out to be signal peptides.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
44
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
45 One of the most common mistakes by the program is to reverse the direction of proteins with one TM segment.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
46
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
47 Do not use the program to predict whether a non-membrane protein is cytoplasmic or not.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
48
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
49 **Notes**
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
50
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
51 The raw output from TMHMM v2.0 looks like this (six columns tab separated):
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
52
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
53 =================================== ======= =========== ============= ========= =============================
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
54 gi|2781234|pdb|1JLY|B len=304 ExpAA=0.01 First60=0.00 PredHel=0 Topology=o
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
55 gi|4959044|gb|AAD34209.1|AF069992_1 len=600 ExpAA=0.00 First60=0.00 PredHel=0 Topology=o
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
56 gi|671626|emb|CAA85685.1| len=473 ExpAA=0.19 First60=0.00 PredHel=0 Topology=o
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
57 gi|3298468|dbj|BAA31520.1| len=107 ExpAA=59.37 First60=31.17 PredHel=3 Topology=o23-45i52-74o89-106i
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
58 =================================== ======= =========== ============= ========= =============================
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
59
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
60 In order to make it easier to use in Galaxy, the wrapper script simplifies this to remove the redundant tags, and instead adds a comment line at the top with the column names:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
61
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
62 =================================== === ===== ======= ======= ====================
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
63 #ID len ExpAA First60 PredHel Topology
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
64 gi|2781234|pdb|1JLY|B 304 0.01 0.00 0 o
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
65 gi|4959044|gb|AAD34209.1|AF069992_1 600 0.00 0.00 0 o
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
66 gi|671626|emb|CAA85685.1| 473 0.19 0.00 0 o
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
67 gi|3298468|dbj|BAA31520.1| 107 59.37 31.17 3 o23-45i52-74o89-106i
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
68 =================================== === ===== ======= ======= ====================
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
69
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
70 **References**
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
71
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
72 Krogh, Larsson, von Heijne, and Sonnhammer.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
73 Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
74 J. Mol. Biol. 305:567-580, 2001.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
75
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
76 Sonnhammer, von Heijne, and Krogh.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
77 A hidden Markov model for predicting transmembrane helices in protein sequences.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
78 In J. Glasgow et al., eds.: Proc. Sixth Int. Conf. on Intelligent Systems for Molecular Biology, pages 175-182. AAAI Press, 1998.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
79
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
80 </help>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
81 </tool>