tmhmm_and_signalp: tools/protein_analysis/signalp3.xml annotate

annotate tools/protein_analysis/signalp3.xml @ 33:4fcc441269f5 draft

"This is v0.2.12 with black formating and Python 3 next fix etc"

author	peterjc
date	Thu, 17 Jun 2021 08:33:07 +0000
parents	20da7f48b56f
children	7a2e20baacee

rev	line source
30 6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 26 diff changeset	1 <tool id="signalp3" name="SignalP 3.0" version="0.0.19">
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="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	8 </requirements>
30 6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 26 diff changeset	9 <version_command>
6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 26 diff changeset	10 python $__tool_directory__/signalp3.py --version
6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 26 diff changeset	11 </version_command>
6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 26 diff changeset	12 <command detect_errors="aggressive">
6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 26 diff changeset	13 python $__tool_directory__/signalp3.py $organism $truncate "\$GALAXY_SLOTS" '$fasta_file' '$tabular_file'
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	14 </command>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	15 <inputs>
30 6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 26 diff changeset	16 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	17 <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	18 <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	19 <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	20 <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	21 </param>
4 1426b2bae76d Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository peterjc parents: 3 diff changeset	22 <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	23 <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	24 </param>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	25 </inputs>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	26 <outputs>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	27 <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	28 </outputs>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	29 <tests>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	30 <test>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	31 <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	32 <param name="organism" value="euk"/>
30 6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 26 diff changeset	33 <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	34 <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	35 </test>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	36 <test>
9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	37 <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	38 <param name="organism" value="euk"/>
30 6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 26 diff changeset	39 <param name="truncate" value="60"/>
1 9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	40 <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	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 <test>
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="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	44 <param name="organism" value="gram+"/>
30 6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 26 diff changeset	45 <param name="truncate" value="80"/>
1 9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	46 <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	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 <test>
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="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	50 <param name="organism" value="gram-"/>
30 6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 26 diff changeset	51 <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	52 <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	53 </test>
4 1426b2bae76d Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository peterjc parents: 3 diff changeset	54 <test>
1426b2bae76d Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository peterjc parents: 3 diff changeset	55 <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	56 <param name="organism" value="euk"/>
30 6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 26 diff changeset	57 <param name="truncate" value="70"/>
4 1426b2bae76d Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository peterjc parents: 3 diff changeset	58 <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	59 </test>
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	60 </tests>
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	61 <help>
30 6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 26 diff changeset	62
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	63 What it does
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	64
1 9a8a7f680dd6 Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	65 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	66
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	67 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	68
8 391a142c1e60 Uploaded peterjc parents: 7 diff changeset	69 ====== =================================================
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	70 Column Description
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	71 ------ -------------------------------------------------
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	72 1 Sequence identifier
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	73 2-14 Neural Network (NN) predictions (13 columns)
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	74 15-20 Hidden Markov Model (HMM) predictions (6 columns)
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	75 ====== =================================================
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	76
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	77 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	78
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	79 Neural Network Scores
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	80
30 6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 26 diff changeset	81 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.
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	82
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	83 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	84
8 391a142c1e60 Uploaded peterjc parents: 7 diff changeset	85 ====== ======= ===============================================================
30 6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 26 diff changeset	86 Column Name Description
8 391a142c1e60 Uploaded peterjc parents: 7 diff changeset	87 ------ ------- ---------------------------------------------------------------
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	88 2-4 C-score The C-score is the 'cleavage site' score. For each position in
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	89 the submitted sequence, a C-score is reported, which should
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	90 only be significantly high at the cleavage site. Confusion is
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	91 often seen with the position numbering of the cleavage site.
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	92 When a cleavage site position is referred to by a single number,
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	93 the number indicates the first residue in the mature protein,
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	94 meaning, that a predicted cleavage site between amino acid 26-27
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	95 is reported as 27, corresponding to the mature protein starting
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	96 at (and including) position 27.
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	97 ------ ------- ---------------------------------------------------------------
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	98 5-7 S-score The S-score for the signal peptide prediction is calculated for
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	99 every single amino acid position in the submitted sequence (not
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	100 shown in the output via Galaxy), with high scores indicating
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	101 that the corresponding amino acid is part of a signal peptide,
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	102 and low scores indicating that the amino acid is part of a
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	103 mature protein.
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	104 ------ ------- ---------------------------------------------------------------
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	105 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	106 resulting in a better cleavage site prediction than the raw
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	107 C-score alone. This is due to the fact that multiple high-peaking
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	108 C-scores can be found in one sequence, where only one is the
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	109 true cleavage site. The cleavage site is assigned from the
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	110 Y-score where the slope of the S-score is steep and a
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	111 significant C-score is found.
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	112 ------ ------- ---------------------------------------------------------------
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	113 11-12 S-mean The S-mean is the average of the S-score, ranging from the
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	114 N-terminal amino acid to the amino acid assigned with the
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	115 highest Y-max score, thus the S-mean score is calculated for
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	116 the length of the predicted signal peptide. The S-mean score
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	117 was in SignalP version 2.0 used as the criteria for
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	118 discrimination of secretory and non-secretory proteins.
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	119 ------ ------- ---------------------------------------------------------------
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	120 13-14 D-score The D-score was introduced in SignalP version 3.0 and is a
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	121 simple average of the S-mean and Y-max score. The score shows
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	122 superior discrimination performance of secretory and
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	123 non-secretory proteins to that of the S-mean score which was
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	124 used in SignalP version 1 and 2.
391a142c1e60 Uploaded peterjc parents: 7 diff changeset	125 ====== ======= ===============================================================
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	126
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	127 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	128
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	129 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	130
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	131 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	132
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	133 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	134
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	135 Notes
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	136
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	137 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	138
30 6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 26 diff changeset	139 ==================== ===== === = ===== === = ===== === = ===== = ===== = =================================== = ===== === = ===== =
6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 26 diff changeset	140 # SignalP-NN euk predictions # SignalP-HMM euk predictions
6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 26 diff changeset	141 ----------------------------------------------------------------------------- ------------------------------------------------------------
6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 26 diff changeset	142 # name Cmax pos ? Ymax pos ? Smax pos ? Smean ? D ? # name ! Cmax pos ? Sprob ?
6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 26 diff changeset	143 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
6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 26 diff changeset	144 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
6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 26 diff changeset	145 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
6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 26 diff changeset	146 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
6d9d7cdf00fc v0.2.11 Job splitting fast-fail; RXLR tools supports HMMER2 from BioConda; Capture more version information; misc internal changes peterjc parents: 26 diff changeset	147 ==================== ===== === = ===== === = ===== === = ===== = ===== = =================================== = ===== === = ===== =
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	148
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	149 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	150
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	151 =================================== ============= =========== ============ ============= =========== ============ ============= =========== ============ ============== ============= ========== ========= ======== ============== ============ ============= =============== ==============
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	152 #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	153 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	154 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	155 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	156 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	157 =================================== ============= =========== ============ ============= =========== ============ ============= =========== ============ ============== ============= ========== ========= ======== ============== ============ ============= =============== ==============
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	158
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	159 Truncation
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	160
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	161 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	162
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	163 References
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	164
20 a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information. peterjc parents: 19 diff changeset	165 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	166 cite the following papers:
a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information. peterjc parents: 19 diff changeset	167
22 90e3d02f8013 Uploaded v0.2.5 preview 6, can use accents in <help> RST peterjc parents: 20 diff changeset	168 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	169 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	170 in molecular plant pathology. PeerJ 1:e167
32 20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	171 https://doi.org/10.7717/peerj.167
20 a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information. peterjc parents: 19 diff changeset	172
a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information. peterjc parents: 19 diff changeset	173 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	174 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	175 J. Mol. Biol., 340:783-795.
32 20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	176 https://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	177
20 a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information. peterjc parents: 19 diff changeset	178 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	179 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	180 Protein Engineering, 10:1-6.
32 20da7f48b56f "Check this is up to date with all 2020 changes" peterjc parents: 30 diff changeset	181 https://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	182
20 a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information. peterjc parents: 19 diff changeset	183 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	184 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	185 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	186 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	187 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	188
20 a538e182fab3 Uploaded v0.2.5 preview 4, adding Cock et al. 2003 citation information. peterjc parents: 19 diff changeset	189 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	190
17 af3174637834 Uploaded v0.2.5 preview 1, adding links to Tool Shed entry peterjc parents: 8 diff changeset	191 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	192 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	193 </help>
25 41a42022f815 Uploaded v0.2.6, embedded citations peterjc parents: 22 diff changeset	194 <citations>
41a42022f815 Uploaded v0.2.6, embedded citations peterjc parents: 22 diff changeset	195 <citation type="doi">10.7717/peerj.167</citation>
41a42022f815 Uploaded v0.2.6, embedded citations peterjc parents: 22 diff changeset	196 <citation type="doi">10.1016/j.jmb.2004.05.028</citation>
41a42022f815 Uploaded v0.2.6, embedded citations peterjc parents: 22 diff changeset	197 <citation type="doi">10.1093/protein/10.1.1</citation>
41a42022f815 Uploaded v0.2.6, embedded citations peterjc parents: 22 diff changeset	198 <!-- TODO - Add bibtex entry for PMID: 9783217 -->
41a42022f815 Uploaded v0.2.6, embedded citations peterjc parents: 22 diff changeset	199 </citations>
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	200 </tool>

Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/signalp3.xml @ 33:4fcc441269f5 draft