Mercurial > repos > peterjc > tmhmm_and_signalp

comparison tools/protein_analysis/tmhmm2.xml @ 1:3ff1dcbb9440

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Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 18:04:05 -0400
parents bca9bc7fdaef
children 6901298ac16c
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0:bca9bc7fdaef 1:3ff1dcbb9440
1 <tool id="tmhmm2" name="TMHMM 2.0" version="0.0.1"> 1 <tool id="tmhmm2" name="TMHMM 2.0" version="0.0.3">
2 <description>Find transmembrane domains in protein sequences</description> 2 <description>Find transmembrane domains in protein sequences</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 tmhmm2.py 8 $fasta_file $tabular_file 4 tmhmm2.py 8 $fasta_file $tabular_file
5 ##I want the number of threads to be a Galaxy config option... 5 ##I want the number of threads to be a Galaxy config option...
6 </command> 6 </command>
20 <requirement type="binary">tmhmm</requirement> 20 <requirement type="binary">tmhmm</requirement>
21 </requirements> 21 </requirements>
22 <tests> 22 <tests>
23 <test> 23 <test>
24 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta"/> 24 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta"/>
25 <output name="tabular_file" file="four_human_proteins.tmhmm2.tsv" ftype="tabular"/> 25 <output name="tabular_file" file="four_human_proteins.tmhmm2.tabular" ftype="tabular"/>
26 </test>
27 <test>
28 <param name="fasta_file" value="empty.fasta" ftype="fasta"/>
29 <output name="tabular_file" file="empty_tmhmm2.tabular" ftype="tabular"/>
26 </test> 30 </test>
27 </tests> 31 </tests>
28 <help> 32 <help>
29 33
30 **What it does** 34 **What it does**
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). 42 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).
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. 43 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.
40 5. Number of transmembrane helices predicted by N-best. 44 5. Number of transmembrane helices predicted by N-best.
41 6. Topology predicted by N-best (encoded as a strip using o for output and i for inside) 45 6. Topology predicted by N-best (encoded as a strip using o for output and i for inside)
42 46
43 Predicted TM segments in the n-terminal region sometime turn out to be signal peptides. 47 Predicted TM segments in the n-terminal region sometimes turn out to be signal peptides.
44 48
45 One of the most common mistakes by the program is to reverse the direction of proteins with one TM segment. 49 One of the most common mistakes by the program is to reverse the direction of proteins with one TM segment (i.e. mixing up which end of the protein is outside and inside the membrane).
46 50
47 Do not use the program to predict whether a non-membrane protein is cytoplasmic or not. 51 Do not use the program to predict whether a non-membrane protein is cytoplasmic or not.
48 52
49 **Notes** 53 **Notes**
50 54