Mercurial > repos > peterjc > tmhmm_and_signalp
diff tools/protein_analysis/wolf_psort.xml @ 5:0f1c61998b22
Migrated tool version 0.0.8 from old tool shed archive to new tool shed repository
author | peterjc |
---|---|
date | Tue, 07 Jun 2011 18:06:27 -0400 |
parents | |
children | a290c6d4e658 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/protein_analysis/wolf_psort.xml Tue Jun 07 18:06:27 2011 -0400 @@ -0,0 +1,102 @@ +<tool id="wolf_psort" name="WoLF PSORT" version="0.0.1"> + <description>Eukaryote protein subcellular localization prediction</description> + <command interpreter="python"> + wolf_psort.py $organism 8 $fasta_file $tabular_file + ##I want the number of threads to be a Galaxy config option... + </command> + <inputs> + <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="animal">Animal</option> + <option value="plant">Plant</option> + <option value="fungi">Fungi</option> + </param> + </inputs> + <outputs> + <data name="tabular_file" format="tabular" label="WoLF PSORT $organism results" /> + </outputs> + <requirements> + <requirement type="binary">runWolfPsortSummary</requirement> + </requirements> + <help> + +**What it does** + +This calls the WoLF PSORT tool for prediction of eukaryote protein subcellular localization. + +The input is a FASTA file of protein sequences, and the output is tabular with four columns (multiple rows per protein): + + * Sequence identifier + * Compartment + * Score + * Prediction rank + + +**Localization Compartments** + +The table below gives the WoLF PSORT localization site definitions, and the corresponding Gene Ontology (GO) term. + +====== ===================== ===================== +Abbrev Localization Site GO Cellular Component +------ --------------------- --------------------- +chlo chloroplast 0009507, 0009543 +cyto cytosol 0005829 +cysk cytoskeleton 0005856(2) +E.R. endoplasmic reticulum 0005783 +extr extracellular 0005576, 0005618 +golg Golgi apparatus 0005794(1) +lyso lysosome 0005764 +mito mitochondria 0005739 +nucl nuclear 0005634 +pero peroxisome 0005777(2) +plas plasma membrane 0005886 +vacu vacuolar membrane 0005774(2) +====== ===================== ===================== + +Additionally compound predictions like mito_nucl are also given. + + +**Notes** + +The raw output from WoLF PSORT looks like this (space separated), showing two proteins: + +================================ ============================================ +gi|301087619|ref|XP_002894699.1| extr 12, mito 4, E.R. 3, golg 3, mito_nucl 3 +gi|301087623|ref|XP_002894700.1| extr 21, mito 2, cyto 2, cyto_mito 2 +================================ ============================================ + +This is reformatted into a tabular file as follows for use in Galaxy: + +================================ =========== ===== ==== +#ID Compartment Score Rank +-------------------------------- ----------- ----- ---- +gi|301087619|ref|XP_002894699.1| extr 12 1 +gi|301087619|ref|XP_002894699.1| mito 4 2 +gi|301087619|ref|XP_002894699.1| E.R. 3 3 +gi|301087619|ref|XP_002894699.1| golg 3 4 +gi|301087619|ref|XP_002894699.1| mito_nucl 3 5 +gi|301087623|ref|XP_002894700.1| extr 21 1 +gi|301087623|ref|XP_002894700.1| mito 2 2 +gi|301087623|ref|XP_002894700.1| cyto 2 3 +gi|301087623|ref|XP_002894700.1| cyto_mito 2 4 +================================ =========== ===== ==== + +This way you can easily filter for things like having a top prediction for +mitochondria (c2=='mito' and c4==1), or extracellular with a score of at +least 10 (c2=='extr' and 10<=c3), and so on. + + +**References** + +Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C.J. Adams-Collier, and Kenta Nakai, +WoLF PSORT: Protein Localization Predictor. +Nucleic Acids Research, 35(S2), W585-W587, doi:10.1093/nar/gkm259, 2007. + +Paul Horton, Keun-Joon Park, Takeshi Obayashi and Kenta Nakai. +Protein Subcellular Localization Prediction with WoLF PSORT. +Proceedings of the 4th Annual Asia Pacific Bioinformatics Conference APBC06, Taipei, Taiwan. pp. 39-48, 2006. + +http://wolfpsort.org + + </help> +</tool>