tmhmm_and_signalp: tools/protein_analysis/signalp3.xml annotate

annotate tools/protein_analysis/signalp3.xml @ 27:9e36a1b9302d draft

planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 3c6f0dca0e1318eecd1e07d177ffc5752b4f6c95

author	peterjc
date	Thu, 21 May 2015 10:57:40 -0400
parents	20139cb4c844
children	6d9d7cdf00fc

rev	line source
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 25 diff changeset	1 <tool id="signalp3" name="SignalP 3.0" version="0.0.15">
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	2 <description>Find signal peptides in protein sequences</description>
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	3 <!-- If job splitting is enabled, break up the query file into parts -->
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	4 <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal -->
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	5 <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
26 20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 25 diff changeset	6 <requirements>
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 25 diff changeset	7 <requirement type="binary">signalp</requirement>
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 25 diff changeset	8 <requirement type="package">signalp</requirement>
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 25 diff changeset	9 </requirements>
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 25 diff changeset	10 <stdio>
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 25 diff changeset	11 <!-- Anything other than zero is an error -->
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 25 diff changeset	12 <exit_code range="1:" />
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 25 diff changeset	13 <exit_code range=":-1" />
20139cb4c844 planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/protein_analysis commit 221d4187992cbb993e02dc3ea0ef0150c7916a4a-dirty peterjc parents: 25 diff changeset	14 </stdio>
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	15 <command interpreter="python">
25 41a42022f815 Uploaded v0.2.6, embedded citations peterjc parents: 22 diff changeset	16 signalp3.py $organism $truncate "\$GALAXY_SLOTS" $fasta_file $tabular_file
19 4cd848c5590b Uploaded v0.2.5 preview 3, use $NSLOTS in the PSORT wrappers. peterjc parents: 17 diff changeset	17 ##If the environment variable isn't set, get "", and the python wrapper
4cd848c5590b Uploaded v0.2.5 preview 3, use $NSLOTS in the PSORT wrappers. peterjc parents: 17 diff changeset	18 ##defaults to four threads.
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	19 </command>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	20 <inputs>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	21 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	22 <param name="organism" type="select" display="radio" label="Organism">
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	23 <option value="euk">Eukaryote</option>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	24 <option value="gram+">Gram positive</option>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	25 <option value="gram-">Gram negative</option>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	26 </param>
4 1426b2bae76d Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository peterjc parents: 3 diff changeset	27 <param name="truncate" type="integer" label="Truncate sequences to this many amino acids" value="70" help="Use zero for no truncation, maximum value 6000">
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	28 <validator type="in_range" min="0" max="6000" message="Truncation value should be at most 6000. Use zero for no truncation."/>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	29 </param>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	30 </inputs>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	31 <outputs>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	32 <data name="tabular_file" format="tabular" label="SignalP $organism results" />
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	33 </outputs>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	34 <tests>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	35 <test>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	36 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta"/>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	37 <param name="organism" value="euk"/>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	38 <param name="truncate" value="0"/>
1 9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	39 <output name="tabular_file" file="four_human_proteins.signalp3.tabular" ftype="tabular"/>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	40 </test>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	41 <test>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	42 <param name="fasta_file" value="empty.fasta" ftype="fasta"/>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	43 <param name="organism" value="euk"/>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	44 <param name="truncate" value="60"/>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	45 <output name="tabular_file" file="empty_signalp3.tabular" ftype="tabular"/>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	46 </test>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	47 <test>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	48 <param name="fasta_file" value="empty.fasta" ftype="fasta"/>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	49 <param name="organism" value="gram+"/>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	50 <param name="truncate" value="80"/>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	51 <output name="tabular_file" file="empty_signalp3.tabular" ftype="tabular"/>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	52 </test>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	53 <test>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	54 <param name="fasta_file" value="empty.fasta" ftype="fasta"/>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	55 <param name="organism" value="gram-"/>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	56 <param name="truncate" value="0"/>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	57 <output name="tabular_file" file="empty_signalp3.tabular" ftype="tabular"/>
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	58 </test>
4 1426b2bae76d Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository peterjc parents: 3 diff changeset	59 <test>
1426b2bae76d Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository peterjc parents: 3 diff changeset	60 <param name="fasta_file" value="rxlr_win_et_al_2007.fasta" ftype="fasta"/>
1426b2bae76d Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository peterjc parents: 3 diff changeset	61 <param name="organism" value="euk"/>
1426b2bae76d Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository peterjc parents: 3 diff changeset	62 <param name="truncate" value="70"/>
1426b2bae76d Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository peterjc parents: 3 diff changeset	63 <output name="tabular_file" file="rxlr_win_et_al_2007_sp3.tabular" ftype="tabular"/>
1426b2bae76d Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository peterjc parents: 3 diff changeset	64 </test>
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	65 </tests>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	66 <help>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	67
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	68 What it does
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	69
1 9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	70 This calls the SignalP v3.0 tool for prediction of signal peptides, which uses both a Neural Network (NN) and Hidden Markov Model (HMM) to produce two sets of scores.
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	71
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	72 The input is a FASTA file of protein sequences, and the output is tabular with twenty columns (one row per protein):
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	73
8 391a142c1e60 Uploaded peterjc parents: 7 diff changeset	74 ====== =================================================
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	75 Column Description
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	76 ------ -------------------------------------------------
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	77 1 Sequence identifier
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	78 2-14 Neural Network (NN) predictions (13 columns)
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	79 15-20 Hidden Markov Model (HMM) predictions (6 columns)
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	80 ====== =================================================
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	81
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	82 Internally the input FASTA file is divided into parts (to allow multiple processors to be used), and the proteins truncated as specified (see below). The raw output from SignalP is then reformatted into a tabular layout suitable for Galaxy (see below).
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	83
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	84 Neural Network Scores
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	85
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	86 For each organism class (Eukaryote, Gram-negative and Gram-positive), two different neural networks are used, one for predicting the actual signal peptide and one for predicting the position of the signal peptidase I (SPase I) cleavage site.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	87
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	88 The NN output comprises three different scores (C-max, S-max and Y-max) and two scores derived from them (S-mean and D-score).
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	89
8 391a142c1e60 Uploaded peterjc parents: 7 diff changeset	90 ====== ======= ===============================================================
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	91 Column Name Description
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	92 ------ ------- ---------------------------------------------------------------
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	93 2-4 C-score The C-score is the 'cleavage site' score. For each position in
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	94 the submitted sequence, a C-score is reported, which should
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	95 only be significantly high at the cleavage site. Confusion is
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	96 often seen with the position numbering of the cleavage site.
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	97 When a cleavage site position is referred to by a single number,
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	98 the number indicates the first residue in the mature protein,
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	99 meaning, that a predicted cleavage site between amino acid 26-27
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	100 is reported as 27, corresponding to the mature protein starting
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	101 at (and including) position 27.
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	102 ------ ------- ---------------------------------------------------------------
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	103 5-7 S-score The S-score for the signal peptide prediction is calculated for
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	104 every single amino acid position in the submitted sequence (not
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	105 shown in the output via Galaxy), with high scores indicating
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	106 that the corresponding amino acid is part of a signal peptide,
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	107 and low scores indicating that the amino acid is part of a
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	108 mature protein.
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	109 ------ ------- ---------------------------------------------------------------
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	110 8-10 Y-max Y-max is a derivative of the C-score combined with the S-score
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	111 resulting in a better cleavage site prediction than the raw
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	112 C-score alone. This is due to the fact that multiple high-peaking
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	113 C-scores can be found in one sequence, where only one is the
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	114 true cleavage site. The cleavage site is assigned from the
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	115 Y-score where the slope of the S-score is steep and a
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	116 significant C-score is found.
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	117 ------ ------- ---------------------------------------------------------------
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	118 11-12 S-mean The S-mean is the average of the S-score, ranging from the
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	119 N-terminal amino acid to the amino acid assigned with the
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	120 highest Y-max score, thus the S-mean score is calculated for
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	121 the length of the predicted signal peptide. The S-mean score
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	122 was in SignalP version 2.0 used as the criteria for
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	123 discrimination of secretory and non-secretory proteins.
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	124 ------ ------- ---------------------------------------------------------------
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	125 13-14 D-score The D-score was introduced in SignalP version 3.0 and is a
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	126 simple average of the S-mean and Y-max score. The score shows
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	127 superior discrimination performance of secretory and
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	128 non-secretory proteins to that of the S-mean score which was
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	129 used in SignalP version 1 and 2.
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	130 ====== ======= ===============================================================
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	131
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	132 For non-secretory proteins all the scores represented in the SignalP3-NN output should ideally be very low.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	133
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	134 Hidden Markov Model Scores
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	135
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	136 The hidden Markov model calculates the probability of whether the submitted sequence contains a signal peptide or not. The eukaryotic HMM model also reports the probability of a signal anchor, previously named uncleaved signal peptides. Furthermore, the cleavage site is assigned by a probability score together with scores for the n-region, h-region, and c-region of the signal peptide, if such one is found.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	137
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	138 The 'type' column uses 'S' for a signal peptide (i.e. secretory protein) and 'Q' for non-secretory protein.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	139
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	140 Notes
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	141
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	142 The raw output 'short' output from TMHMM v2.0 looks something like this (21 columns space separated - shown here formatted nicely). Notice that the identifiers are given twice, the first time truncated (as part of the NN predictions) and the second time in full (in the HMM predictions).
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	143
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	144 ==================== ===== === = ===== === = ===== === = ===== = ===== = =================================== = ===== === = ===== =
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	145 # SignalP-NN euk predictions # SignalP-HMM euk predictions
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	146 ----------------------------------------------------------------------------- ------------------------------------------------------------
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	147 # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? D ? # name ! Cmax pos ? Sprob ?
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	148 gi\|2781234\|pdb\|1JLY\| 0.061 17 N 0.043 17 N 0.199 1 N 0.067 N 0.055 N gi\|2781234\|pdb\|1JLY\|B Q 0.000 17 N 0.000 N
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	149 gi\|4959044\|gb\|AAD342 0.099 191 N 0.012 38 N 0.023 12 N 0.014 N 0.013 N gi\|4959044\|gb\|AAD34209.1\|AF069992_1 Q 0.000 0 N 0.000 N
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	150 gi\|671626\|emb\|CAA856 0.139 381 N 0.020 8 N 0.121 4 N 0.067 N 0.044 N gi\|671626\|emb\|CAA85685.1\| Q 0.000 0 N 0.000 N
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	151 gi\|3298468\|dbj\|BAA31 0.208 24 N 0.184 38 N 0.980 32 Y 0.613 Y 0.398 N gi\|3298468\|dbj\|BAA31520.1\| Q 0.066 24 N 0.139 N
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	152 ==================== ===== === = ===== === = ===== === = ===== = ===== = =================================== = ===== === = ===== =
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	153
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	154 In order to make this easier to use in Galaxy, the wrapper script simplifies this to remove the redundant column and use tabs for separation. It also includes a header line with unique column names.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	155
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	156 =================================== ============= =========== ============ ============= =========== ============ ============= =========== ============ ============== ============= ========== ========= ======== ============== ============ ============= =============== ==============
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	157 #ID NN_Cmax_score NN_Cmax_pos NN_Cmax_pred NN_Ymax_score NN_Ymax_pos NN_Ymax_pred NN_Smax_score NN_Smax_pos NN_Smax_pred NN_Smean_score NN_Smean_pred NN_D_score NN_D_pred HMM_type HMM_Cmax_score HMM_Cmax_pos HMM_Cmax_pred HMM_Sprob_score HMM_Sprob_pred
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	158 gi\|2781234\|pdb\|1JLY\|B 0.061 17 N 0.043 17 N 0.199 1 N 0.067 N 0.055 N Q 0.000 17 N 0.000 N
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	159 gi\|4959044\|gb\|AAD34209.1\|AF069992_1 0.099 191 N 0.012 38 N 0.023 12 N 0.014 N 0.013 N Q 0.000 0 N 0.000 N
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	160 gi\|671626\|emb\|CAA85685.1\| 0.139 381 N 0.020 8 N 0.121 4 N 0.067 N 0.044 N Q 0.000 0 N 0.000 N
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	161 gi\|3298468\|dbj\|BAA31520.1\| 0.208 24 N 0.184 38 N 0.980 32 Y 0.613 Y 0.398 N Q 0.066 24 N 0.139 N
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	162 =================================== ============= =========== ============ ============= =========== ============ ============= =========== ============ ============== ============= ========== ========= ======== ============== ============ ============= =============== ==============
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	163
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	164 Truncation
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	165
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	166 Signal peptides are found at the start of a protein, so there is limited value in providing the full length sequence, and providing the full sequence slows down the analysis. Furthermore, SignalP has an upper bound on the sequence length it will accept (6000bp). Thus for practical reasons it is useful to truncate the proteins before passing them to SignalP. However, the precise point they are truncated does have a small influence on some score values, and thus to the results.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	167
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	168 References
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	169
20 a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information. peterjc parents: 19 diff changeset	170 If you use this Galaxy tool in work leading to a scientific publication please
a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information. peterjc parents: 19 diff changeset	171 cite the following papers:
a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information. peterjc parents: 19 diff changeset	172
22 90e3d02f8013 Uploaded v0.2.5 preview 6, can use accents in <help> RST peterjc parents: 20 diff changeset	173 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
20 a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information. peterjc parents: 19 diff changeset	174 Galaxy tools and workflows for sequence analysis with applications
a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information. peterjc parents: 19 diff changeset	175 in molecular plant pathology. PeerJ 1:e167
a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information. peterjc parents: 19 diff changeset	176 http://dx.doi.org/10.7717/peerj.167
a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information. peterjc parents: 19 diff changeset	177
a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information. peterjc parents: 19 diff changeset	178 Bendtsen, Nielsen, von Heijne, and Brunak (2004).
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	179 Improved prediction of signal peptides: SignalP 3.0.
20 a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information. peterjc parents: 19 diff changeset	180 J. Mol. Biol., 340:783-795.
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	181 http://dx.doi.org/10.1016/j.jmb.2004.05.028
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	182
20 a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information. peterjc parents: 19 diff changeset	183 Nielsen, Engelbrecht, Brunak and von Heijne (1997).
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	184 Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.
20 a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information. peterjc parents: 19 diff changeset	185 Protein Engineering, 10:1-6.
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	186 http://dx.doi.org/10.1093/protein/10.1.1
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	187
20 a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information. peterjc parents: 19 diff changeset	188 Nielsen and Krogh (1998).
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	189 Prediction of signal peptides and signal anchors by a hidden Markov model.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	190 Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB 6),
20 a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information. peterjc parents: 19 diff changeset	191 AAAI Press, Menlo Park, California, pp. 122-130.
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: 4 diff changeset	192 http://www.ncbi.nlm.nih.gov/pubmed/9783217
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	193
20 a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information. peterjc parents: 19 diff changeset	194 See also http://www.cbs.dtu.dk/services/SignalP-3.0/output.php
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	195
17 af3174637834 Uploaded v0.2.5 preview 1, adding links to Tool Shed entry peterjc parents: 8 diff changeset	196 This wrapper is available to install into other Galaxy Instances via the Galaxy
af3174637834 Uploaded v0.2.5 preview 1, adding links to Tool Shed entry peterjc parents: 8 diff changeset	197 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	198 </help>
25 41a42022f815 Uploaded v0.2.6, embedded citations peterjc parents: 22 diff changeset	199 <citations>
41a42022f815 Uploaded v0.2.6, embedded citations peterjc parents: 22 diff changeset	200 <citation type="doi">10.7717/peerj.167</citation>
41a42022f815 Uploaded v0.2.6, embedded citations peterjc parents: 22 diff changeset	201 <citation type="doi">10.1016/j.jmb.2004.05.028</citation>
41a42022f815 Uploaded v0.2.6, embedded citations peterjc parents: 22 diff changeset	202 <citation type="doi">10.1093/protein/10.1.1</citation>
41a42022f815 Uploaded v0.2.6, embedded citations peterjc parents: 22 diff changeset	203 <!-- TODO - Add bibtex entry for PMID: 9783217 -->
41a42022f815 Uploaded v0.2.6, embedded citations peterjc parents: 22 diff changeset	204 </citations>
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	205 </tool>

Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/signalp3.xml @ 27:9e36a1b9302d draft