Mercurial > repos > peterjc > tmhmm_and_signalp
comparison tools/protein_analysis/tmhmm2.xml @ 2:6901298ac16c
Migrated tool version 0.0.5 from old tool shed archive to new tool shed repository
author | peterjc |
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date | Tue, 07 Jun 2011 18:04:39 -0400 |
parents | 3ff1dcbb9440 |
children | f3b373a41f81 |
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1:3ff1dcbb9440 | 2:6901298ac16c |
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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 |