Mercurial > repos > peterjc > tmhmm_and_signalp
diff tools/protein_analysis/signalp3.xml @ 20:a19b3ded8f33 draft
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 |
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--- a/tools/protein_analysis/signalp3.xml Wed Feb 01 09:46:42 2017 -0500 +++ b/tools/protein_analysis/signalp3.xml Thu Sep 21 11:35:20 2017 -0400 @@ -1,24 +1,19 @@ -<tool id="signalp3" name="SignalP 3.0" version="0.0.15"> +<tool id="signalp3" name="SignalP 3.0" version="0.0.19"> <description>Find signal peptides in protein sequences</description> <!-- If job splitting is enabled, break up the query file into parts --> <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal --> <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism> <requirements> - <requirement type="binary">signalp</requirement> <requirement type="package">signalp</requirement> </requirements> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> - <command interpreter="python"> - signalp3.py $organism $truncate "\$GALAXY_SLOTS" $fasta_file $tabular_file - ##If the environment variable isn't set, get "", and the python wrapper - ##defaults to four threads. + <version_command> +python $__tool_directory__/signalp3.py --version + </version_command> + <command detect_errors="aggressive"> +python $__tool_directory__/signalp3.py $organism $truncate "\$GALAXY_SLOTS" '$fasta_file' '$tabular_file' </command> <inputs> - <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> + <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> <param name="organism" type="select" display="radio" label="Organism"> <option value="euk">Eukaryote</option> <option value="gram+">Gram positive</option> @@ -35,36 +30,36 @@ <test> <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta"/> <param name="organism" value="euk"/> - <param name="truncate" value="0"/> + <param name="truncate" value="0"/> <output name="tabular_file" file="four_human_proteins.signalp3.tabular" ftype="tabular"/> </test> <test> <param name="fasta_file" value="empty.fasta" ftype="fasta"/> <param name="organism" value="euk"/> - <param name="truncate" value="60"/> + <param name="truncate" value="60"/> <output name="tabular_file" file="empty_signalp3.tabular" ftype="tabular"/> </test> <test> <param name="fasta_file" value="empty.fasta" ftype="fasta"/> <param name="organism" value="gram+"/> - <param name="truncate" value="80"/> + <param name="truncate" value="80"/> <output name="tabular_file" file="empty_signalp3.tabular" ftype="tabular"/> </test> <test> <param name="fasta_file" value="empty.fasta" ftype="fasta"/> <param name="organism" value="gram-"/> - <param name="truncate" value="0"/> + <param name="truncate" value="0"/> <output name="tabular_file" file="empty_signalp3.tabular" ftype="tabular"/> </test> <test> <param name="fasta_file" value="rxlr_win_et_al_2007.fasta" ftype="fasta"/> <param name="organism" value="euk"/> - <param name="truncate" value="70"/> + <param name="truncate" value="70"/> <output name="tabular_file" file="rxlr_win_et_al_2007_sp3.tabular" ftype="tabular"/> </test> </tests> <help> - + **What it does** 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. @@ -83,12 +78,12 @@ **Neural Network Scores** -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. +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. 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). ====== ======= =============================================================== -Column Name Description +Column Name Description ------ ------- --------------------------------------------------------------- 2-4 C-score The C-score is the 'cleavage site' score. For each position in the submitted sequence, a C-score is reported, which should @@ -141,15 +136,15 @@ 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). -==================== ===== === = ===== === = ===== === = ===== = ===== = =================================== = ===== === = ===== = -# SignalP-NN euk predictions # SignalP-HMM euk predictions ------------------------------------------------------------------------------ ------------------------------------------------------------ -# name Cmax pos ? Ymax pos ? Smax pos ? Smean ? D ? # name ! Cmax pos ? Sprob ? -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 -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 -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 -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 -==================== ===== === = ===== === = ===== === = ===== = ===== = =================================== = ===== === = ===== = +==================== ===== === = ===== === = ===== === = ===== = ===== = =================================== = ===== === = ===== = +# SignalP-NN euk predictions # SignalP-HMM euk predictions +----------------------------------------------------------------------------- ------------------------------------------------------------ +# name Cmax pos ? Ymax pos ? Smax pos ? Smean ? D ? # name ! Cmax pos ? Sprob ? +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 +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 +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 +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 +==================== ===== === = ===== === = ===== === = ===== = ===== = =================================== = ===== === = ===== = 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.