Mercurial > repos > peterjc > tmhmm_and_signalp

comparison tools/protein_analysis/tmhmm2.xml @ 2:6901298ac16c

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Migrated tool version 0.0.5 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 18:04:39 -0400
parents 3ff1dcbb9440
children f3b373a41f81
comparison
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1:3ff1dcbb9440 2:6901298ac16c
1 <tool id="tmhmm2" name="TMHMM 2.0" version="0.0.3"> 1 <tool id="tmhmm2" name="TMHMM 2.0" version="0.0.5">
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>
50 50
51 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.
52 52
53 **Notes** 53 **Notes**
54 54
55 The raw output from TMHMM v2.0 looks like this (six columns tab separated): 55 The short format output from TMHMM v2.0 looks like this (six columns tab separated, shown here as a table):
56 56
57 =================================== ======= =========== ============= ========= ============================= 57 =================================== ======= =========== ============= ========= =============================
58 gi|2781234|pdb|1JLY|B len=304 ExpAA=0.01 First60=0.00 PredHel=0 Topology=o 58 gi|2781234|pdb|1JLY|B len=304 ExpAA=0.01 First60=0.00 PredHel=0 Topology=o
59 gi|4959044|gb|AAD34209.1|AF069992_1 len=600 ExpAA=0.00 First60=0.00 PredHel=0 Topology=o 59 gi|4959044|gb|AAD34209.1|AF069992_1 len=600 ExpAA=0.00 First60=0.00 PredHel=0 Topology=o
60 gi|671626|emb|CAA85685.1| len=473 ExpAA=0.19 First60=0.00 PredHel=0 Topology=o 60 gi|671626|emb|CAA85685.1| len=473 ExpAA=0.19 First60=0.00 PredHel=0 Topology=o