Mercurial > repos > peterjc > tmhmm_and_signalp

comparison tools/protein_analysis/tmhmm2.xml @ 20:a19b3ded8f33 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes
author peterjc
date Thu, 21 Sep 2017 11:35:20 -0400
parents eb6ac44d4b8e
children 238eae32483c
comparison
equal deleted inserted replaced
19:f3ecd80850e2 20:a19b3ded8f33
1 <tool id="tmhmm2" name="TMHMM 2.0" version="0.0.14"> 1 <tool id="tmhmm2" name="TMHMM 2.0" version="0.0.16">
2 <description>Find transmembrane domains in protein sequences</description> 2 <description>Find transmembrane domains in protein sequences</description>
3 <!-- If job splitting is enabled, break up the query file into parts --> 3 <!-- If job splitting is enabled, break up the query file into parts -->
4 <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal --> 4 <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal -->
5 <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism> 5 <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
6 <requirements> 6 <requirements>
7 <requirement type="binary">tmhmm</requirement> 7 <requirement type="package">tmhmm2</requirement>
8 <requirement type="package">tmhmm</requirement>
9 </requirements> 8 </requirements>
10 <stdio> 9 <version_command>
11 <!-- Anything other than zero is an error --> 10 python $__tool_directory__/tmhmm2.py --version
12 <exit_code range="1:" /> 11 </version_command>
13 <exit_code range=":-1" /> 12 <command detect_errors="aggressive">
14 </stdio> 13 python $__tool_directory__/tmhmm2.py "\$GALAXY_SLOTS" '$fasta_file' '$tabular_file'
15 <command interpreter="python">
16 tmhmm2.py "\$GALAXY_SLOTS" $fasta_file $tabular_file
17 ##If the environment variable isn't set, get "", and the python wrapper
18 ##defaults to four threads.
19 </command> 14 </command>
20 <inputs> 15 <inputs>
21 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> 16 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
22 <!-- 17 <!--
23 <param name="version" type="select" display="radio" label="Model version"> 18 <param name="version" type="select" display="radio" label="Model version">
24 <option value="">Version 1 (old)</option> 19 <option value="">Version 1 (old)</option>
25 <option value="" selected="True">Version 2 (default)</option> 20 <option value="" selected="true">Version 2 (default)</option>
26 </param> 21 </param>
27 --> 22 -->
28 </inputs> 23 </inputs>
29 <outputs> 24 <outputs>
30 <data name="tabular_file" format="tabular" label="TMHMM results" /> 25 <data name="tabular_file" format="tabular" label="TMHMM results" />
38 <param name="fasta_file" value="empty.fasta" ftype="fasta"/> 33 <param name="fasta_file" value="empty.fasta" ftype="fasta"/>
39 <output name="tabular_file" file="empty_tmhmm2.tabular" ftype="tabular"/> 34 <output name="tabular_file" file="empty_tmhmm2.tabular" ftype="tabular"/>
40 </test> 35 </test>
41 </tests> 36 </tests>
42 <help> 37 <help>
43 38
44 **What it does** 39 **What it does**
45 40
46 This calls the TMHMM v2.0 tool for prediction of transmembrane (TM) helices in proteins using a hidden Markov model (HMM). 41 This calls the TMHMM v2.0 tool for prediction of transmembrane (TM) helices in proteins using a hidden Markov model (HMM).
47 42
48 The input is a FASTA file of protein sequences, and the output is tabular with six columns (one row per protein): 43 The input is a FASTA file of protein sequences, and the output is tabular with six columns (one row per protein):
63 58
64 Predicted TM segments in the n-terminal region sometimes turn out to be signal peptides. 59 Predicted TM segments in the n-terminal region sometimes turn out to be signal peptides.
65 60
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). 61 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).
67 62
68 Do not use the program to predict whether a non-membrane protein is cytoplasmic or not. 63 Do not use the program to predict whether a non-membrane protein is cytoplasmic or not.
69 64
70 65
71 **Notes** 66 **Notes**
72 67
73 The short format output from TMHMM v2.0 looks like this (six columns tab separated, shown here as a table): 68 The short format output from TMHMM v2.0 looks like this (six columns tab separated, shown here as a table):
80 =================================== ======= =========== ============= ========= ============================= 75 =================================== ======= =========== ============= ========= =============================
81 76
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: 77 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:
83 78
84 =================================== === ===== ======= ======= ==================== 79 =================================== === ===== ======= ======= ====================
85 #ID len ExpAA First60 PredHel Topology 80 #ID len ExpAA First60 PredHel Topology
86 gi|2781234|pdb|1JLY|B 304 0.01 0.00 0 o 81 gi|2781234|pdb|1JLY|B 304 0.01 0.00 0 o
87 gi|4959044|gb|AAD34209.1|AF069992_1 600 0.00 0.00 0 o 82 gi|4959044|gb|AAD34209.1|AF069992_1 600 0.00 0.00 0 o
88 gi|671626|emb|CAA85685.1| 473 0.19 0.00 0 o 83 gi|671626|emb|CAA85685.1| 473 0.19 0.00 0 o
89 gi|3298468|dbj|BAA31520.1| 107 59.37 31.17 3 o23-45i52-74o89-106i 84 gi|3298468|dbj|BAA31520.1| 107 59.37 31.17 3 o23-45i52-74o89-106i
90 =================================== === ===== ======= ======= ==================== 85 =================================== === ===== ======= ======= ====================