Mercurial > repos > peterjc > tmhmm_and_signalp
view tools/protein_analysis/wolf_psort.xml @ 17:e6cc27d182a8 draft
Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
| author | peterjc |
|---|---|
| date | Fri, 21 Nov 2014 08:19:09 -0500 |
| parents | 7de64c8b258d |
| children | eb6ac44d4b8e |
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<tool id="wolf_psort" name="WoLF PSORT" version="0.0.8"> <description>Eukaryote protein subcellular localization prediction</description> <command interpreter="python"> wolf_psort.py $organism "\$GALAXY_SLOTS" "$fasta_file" "$tabular_file" ##If the environment variable isn't set, get "", and python wrapper ##defaults to four threads. </command> <stdio> <!-- Anything other than zero is an error --> <exit_code range="1:" /> <exit_code range=":-1" /> </stdio> <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> <tests> <test> <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta"/> <param name="organism" value="animal"/> <output name="tabular_file" file="four_human_proteins.wolf_psort.tabular" ftype="tabular"/> </test> <test> <param name="fasta_file" value="empty.fasta" ftype="fasta"/> <param name="organism" value="animal"/> <output name="tabular_file" file="empty_wolf_psort.tabular" ftype="tabular"/> </test> <test> <param name="fasta_file" value="empty.fasta" ftype="fasta"/> <param name="organism" value="plant"/> <output name="tabular_file" file="empty_wolf_psort.tabular" ftype="tabular"/> </test> <test> <param name="fasta_file" value="empty.fasta" ftype="fasta"/> <param name="organism" value="fungi"/> <output name="tabular_file" file="empty_wolf_psort.tabular" ftype="tabular"/> </test> </tests> <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): ====== =================== Column Description ------ ------------------- 1 Sequence identifier 2 Compartment 3 Score 4 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) ====== ===================== ===================== Numbers in parentheses, such as "0005856(2)" indicate that descendant "part_of" cellular components were also included, up to the specified depth (2 in this case). For example, all of the children and grandchildren of "GO:0005856" were included as "cysk". 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** If you use this Galaxy tool in work leading to a scientific publication please cite the following papers: Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology. PeerJ 1:e167 http://dx.doi.org/10.7717/peerj.167 Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C.J. Adams-Collier, and Kenta Nakai (2007). WoLF PSORT: Protein Localization Predictor. Nucleic Acids Research, 35(S2), W585-W587. http://dx.doi.org/10.1093/nar/gkm259 Paul Horton, Keun-Joon Park, Takeshi Obayashi and Kenta Nakai (2006). Protein Subcellular Localization Prediction with WoLF PSORT. Proceedings of the 4th Annual Asia Pacific Bioinformatics Conference APBC06, Taipei, Taiwan. pp. 39-48. See also http://wolfpsort.org This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp </help> <citations> <citation type="doi">10.7717/peerj.167</citation> <citation type="doi">10.1093/nar/gkm259</citation> </citations> </tool>