Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/tmhmm2.xml @ 18:eb6ac44d4b8e draft

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Suite v0.2.8, record Promoter 2 verion + misc internal updates
author peterjc
date Tue, 01 Sep 2015 09:56:36 -0400
parents e6cc27d182a8
children a19b3ded8f33
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1 <tool id="tmhmm2" name="TMHMM 2.0" version="0.0.14">
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2 <description>Find transmembrane domains in protein sequences</description>
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3 <!-- If job splitting is enabled, break up the query file into parts -->
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4 <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal -->
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5 <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
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6 <requirements>
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7 <requirement type="binary">tmhmm</requirement>
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8 <requirement type="package">tmhmm</requirement>
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9 </requirements>
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10 <stdio>
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11 <!-- Anything other than zero is an error -->
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12 <exit_code range="1:" />
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13 <exit_code range=":-1" />
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14 </stdio>
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15 <command interpreter="python">
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16 tmhmm2.py "\$GALAXY_SLOTS" $fasta_file $tabular_file
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17 ##If the environment variable isn't set, get "", and the python wrapper
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18 ##defaults to four threads.
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19 </command>
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20 <inputs>
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21 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
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22 <!--
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23 <param name="version" type="select" display="radio" label="Model version">
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24 <option value="">Version 1 (old)</option>
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25 <option value="" selected="True">Version 2 (default)</option>
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26 </param>
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27 -->
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28 </inputs>
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29 <outputs>
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30 <data name="tabular_file" format="tabular" label="TMHMM results" />
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta"/>
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35 <output name="tabular_file" file="four_human_proteins.tmhmm2.tabular" ftype="tabular"/>
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36 </test>
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37 <test>
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38 <param name="fasta_file" value="empty.fasta" ftype="fasta"/>
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39 <output name="tabular_file" file="empty_tmhmm2.tabular" ftype="tabular"/>
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40 </test>
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41 </tests>
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42 <help>
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43
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44 **What it does**
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45
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46 This calls the TMHMM v2.0 tool for prediction of transmembrane (TM) helices in proteins using a hidden Markov model (HMM).
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47
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48 The input is a FASTA file of protein sequences, and the output is tabular with six columns (one row per protein):
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49
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50 ====== =====================================================================================
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51 Column Description
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52 ------ -------------------------------------------------------------------------------------
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53 1 Sequence identifier
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54 2 Sequence length
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55 3 Expected number of amino acids in TM helices (ExpAA). If this number is larger than
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56 18 it is very likely to be a transmembrane protein (OR have a signal peptide).
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57 4 Expected number of amino acids in TM helices in the first 60 amino acids of the
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58 protein (Exp60). If this number more than a few, be aware that a predicted
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59 transmembrane helix in the N-term could be a signal peptide.
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60 5 Number of transmembrane helices predicted by N-best.
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61 6 Topology predicted by N-best (encoded as a strip using o for output and i for inside)
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62 ====== =====================================================================================
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63
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64 Predicted TM segments in the n-terminal region sometimes turn out to be signal peptides.
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65
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66 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).
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67
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68 Do not use the program to predict whether a non-membrane protein is cytoplasmic or not.
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69
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70
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71 **Notes**
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72
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73 The short format output from TMHMM v2.0 looks like this (six columns tab separated, shown here as a table):
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74
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75 =================================== ======= =========== ============= ========= =============================
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76 gi|2781234|pdb|1JLY|B len=304 ExpAA=0.01 First60=0.00 PredHel=0 Topology=o
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77 gi|4959044|gb|AAD34209.1|AF069992_1 len=600 ExpAA=0.00 First60=0.00 PredHel=0 Topology=o
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78 gi|671626|emb|CAA85685.1| len=473 ExpAA=0.19 First60=0.00 PredHel=0 Topology=o
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79 gi|3298468|dbj|BAA31520.1| len=107 ExpAA=59.37 First60=31.17 PredHel=3 Topology=o23-45i52-74o89-106i
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80 =================================== ======= =========== ============= ========= =============================
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81
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82 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:
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83
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84 =================================== === ===== ======= ======= ====================
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85 #ID len ExpAA First60 PredHel Topology
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86 gi|2781234|pdb|1JLY|B 304 0.01 0.00 0 o
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87 gi|4959044|gb|AAD34209.1|AF069992_1 600 0.00 0.00 0 o
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88 gi|671626|emb|CAA85685.1| 473 0.19 0.00 0 o
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89 gi|3298468|dbj|BAA31520.1| 107 59.37 31.17 3 o23-45i52-74o89-106i
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90 =================================== === ===== ======= ======= ====================
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91
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92
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93 -----
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94
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95 **References**
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96
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97 If you use this Galaxy tool in work leading to a scientific publication please
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98 cite the following papers:
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99
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100 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
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101 Galaxy tools and workflows for sequence analysis with applications
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102 in molecular plant pathology. PeerJ 1:e167
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103 http://dx.doi.org/10.7717/peerj.167
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104
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105 Krogh, Larsson, von Heijne, and Sonnhammer (2001).
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106 Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes.
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107 J. Mol. Biol. 305:567-580.
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108 http://dx.doi.org/10.1006/jmbi.2000.4315
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109
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110 Sonnhammer, von Heijne, and Krogh (1998).
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111 A hidden Markov model for predicting transmembrane helices in protein sequences.
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112 In J. Glasgow et al., eds.: Proc. Sixth Int. Conf. on Intelligent Systems for Molecular Biology, pages 175-182. AAAI Press.
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113 http://www.ncbi.nlm.nih.gov/pubmed/9783223
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114
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115 See also http://www.cbs.dtu.dk/services/TMHMM/
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116
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117 This wrapper is available to install into other Galaxy Instances via the Galaxy
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118 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
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119 </help>
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120 <citations>
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121 <citation type="doi">10.7717/peerj.167</citation>
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122 <citation type="doi">10.1006/jmbi.2000.4315</citation>
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123 <!-- TODO - add entry for PMID: 9783223 -->
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124 </citations>
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125 </tool>