diff README.rst @ 11:99209ed2ec87 draft

planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/workflows/secreted_protein_workflow commit 4bd49529e9ca2096cd875e98daf7190d13fa8d0b-dirty

--- a/README.rst	Mon Mar 30 11:46:13 2015 -0400
+++ b/README.rst	Wed Feb 01 13:21:32 2017 -0500
@@ -1,180 +1,99 @@
-Introduction
-============
-
-Galaxy is a web-based platform for biological data analysis, supporting
-extension with additional tools (often wrappers for existing command line
-tools) and datatypes. See http://www.galaxyproject.org/ and the public
-server at http://usegalaxy.org for an example.
+This is package is a Galaxy workflow for the identification of candidate
+secreted proteins from a given protein FASTA file.
 
-The NCBI BLAST suite is a widely used set of tools for biological sequence
-comparison. It is available as standalone binaries for use at the command
-line, and via the NCBI website for smaller searches. For more details see
-http://blast.ncbi.nlm.nih.gov/Blast.cgi
+It runs SignalP v3.0 (Bendtsen et al. 2004) and selects only proteins with a
+strong predicted signal peptide, and then runs TMHMM v2.0 (Krogh et al. 2001)
+on those, and selects only proteins without a predicted trans-membrane helix.
+This workflow was used in Kikuchi et al. (2011), and is a simplification of
+the candidate effector protocol described in Jones et al. (2009).
 
-This is an example workflow using the Galaxy wrappers for NCBI BLAST+,
-see https://github.com/peterjc/galaxy_blast
+See http://www.galaxyproject.org for information about the Galaxy Project.
 
 
-Galaxy workflow for counting species of top BLAST hits 
-======================================================
+Availability
+============
 
-This Galaxy workflow (file ``blast_top_hit_species.ga``) is intended for an
-initial assessment of a transcriptome assembly to give a crude indication of
-any major contamination present based on the species of the top BLAST hit
-of 1000 representative sequences.
+This workflow is available to download and/or install from the main
+Galaxy Tool Shed:
 
-.. image:: https://raw.githubusercontent.com/peterjc/galaxy_blast/master/workflows/blast_top_hit_species/blast_top_hit_species.png
-
-In words, the workflow proceeds as follows:
+http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow
 
-1. Upload/import your transcriptome assembly or any nucleotide FASTA file.
-2. Samples 1000 representative sequences, selected uniformly/evenly though
-   the file.
-3. Convert the sampled FASTA file into a three column tabular file.
-4. Runs NCBI BLASTX of the sampled FASTA file against the latest NCBI ``nr``
-   database (assuming this is already available setup on your local Galaxy
-   under the alias ``nr``), requesting tabular output including the taxonomy
-   fields, and at most one matching target sequence.
-5. Remove any duplicate alignments (multiple HSPs for the same match).
-6. Combine the filtered BLAST output with the tabular version of the 1000
-   sequences to give a new tabular file with exactly 1000 lines, adding
-   ``None`` for sequences missing a BLAST hit.
-7. Count the BLAST species names in this file.
-8. Sort the counts.
+Test releases (which should not normally be used) are on the Test Tool Shed:
+
+http://testtoolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow
 
-Finally we would suggest visualising the sorted tally table as a Pie Chart.
+Development is being done on github here:
+
+https://github.com/peterjc/pico_galaxy/tree/master/workflows/secreted_protein_workflow
 
 
 Sample Data
 ===========
 
-As an example, you can upload the transcriptome assembly of the nematode
-*Nacobbus abberans* from Eves van den Akker *et al.* (2015),
-http://dx.doi.org/10.1093/gbe/evu171 using this URL:
-
-http://nematode.net/Data/nacobbus_aberrans_transcript_assembly/N.abberans_reference_no_contam.zip
-
-Running this workflow with a copy of the NCBI non-redundant ``nr`` database
-from 16 Oct 2014 (which did **not** contain this *N. abberans* dataset) gave
-the following results - note 609 out of the 1000 sequences gave no BLAST hit.
-
-===== ==================
-Count Subject Blast Name
------ ------------------
-  609 None
-  244 nematodes
-   30 ascomycetes
-   27 eukaryotes
-    8 basidiomycetes
-    6 aphids
-    5 eudicots
-    5 flies
-  ... ...
-===== ==================
+This workflow was developed and run on several nematode species. For example,
+try the protein set for *Bursaphelenchus xylophilus* (Kikuchi et al. 2011):
 
-As you might guess from	the filename ``N.abberans_reference_no_contam.fasta``,
-this transcriptome assembly has already had obvious contamination removed.
-
-At the time of writing, Galaxy's visualizations could not be included in
-a workflow. You can generate a pie chart from the final count file using
-the counts (c1) and labels (c2), like this:
-
-.. image:: https://raw.githubusercontent.com/peterjc/galaxy_blast/master/workflows/blast_top_hit_species/N_abberans_piechart_mouseover.png
-
-Note the nematode count in this image was shown as a mouse-over effect.
-
-
-Disclaimer
-==========
-
-Species assignment by top BLAST hit is not suitable for any in depth
-analysis. It is particularly prone to false positives where contaminants
-in public datasets are mislabelled. See for example Ed Yong (2015),
-"There's No Plague on the NYC Subway. No Platypuses Either.":
-
-http://phenomena.nationalgeographic.com/2015/02/10/theres-no-plague-on-the-nyc-subway-no-platypuses-either/
-
-
-Known Issues
-============
+ftp://ftp.sanger.ac.uk/pub/pathogens/Bursaphelenchus/xylophilus/Assembly-v1.2/BUX.v1.2.genedb.protein.fa.gz
 
-Counts
-------
-
-This workflow uses the Galaxy "Count" tool, version 1.0.0, as shipped with
-the current stable release (Galaxy v15.03, i.e. March 2015).
-
-The updated "Count" tool version 1.0.1 includes a fix not to remove spaces
-in the fields being counted. In the example above, while the top hits are
-not affected, minor entries like "cellular slime molds" are shown as
-"cellularslimemolds" instead (look closely at the Pie Chart key)..
-
-The updated "Count" tool version 1.0.1 also adds a new option to sort the
-output, which avoids the additional sorting step in the current version of
-the workflow.
-
-A future update to this workflow will use the revised "Count" tool, once
-this is included in the next stable Galaxy release - or migrated to the
-Galaxy Tool Shed.
-
-NCBI nr database
-----------------
-
-The use of external datasets within Galaxy via the ``*.loc`` configuration
-files undermines provenance tracking within Galaxy. This is exacerbated
-by the lack of officially versioned BLAST database releases by the NCBI.
-
-This workflow assumes that you have an entry ``nr`` in your ``blastdb_p.loc``
-(the configuration file listing locally installed BLAST databases external
-to Galaxy - consult the NCBI BLAST+ wrapper documentation for more details),
-and that this points to a mirror of the latest NCBI "non-redundant" database
-from ftp://ftp.ncbi.nlm.nih.gov/blast/db/
-
-i.e. The workflow is intended to be used against the *latest* nr database,
-and thus is not reproducible over the long term as the database changes.
-
-
-Availability
-============
-
-This workflow is available to download and/or install from the main Galaxy Tool Shed:
-
-http://toolshed.g2.bx.psu.edu/view/peterjc/blast_top_hit_species
-
-Test releases (which should not normally be used) are on the Test Tool Shed:
-
-http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast_top_hit_species
-
-Development is being done on github here:
-
-https://github.com/peterjc/galaxy_blast/tree/master/workflows/blast_top_hit_species
+You can upload this directly into Galaxy via this URL. Galaxy will handle
+removing the gzip compression to give you the FASTA protein file which has
+18,074 sequences. The expected result (selecting organism type Eukaryote)
+is a FASTA protein file of 2,297 predicted secreted protein sequences.
 
 
 Citation
 ========
 
-Please cite the following paper (currently available as a preprint):
+If you use this workflow directly, or a derivative of it, in work leading
+to a scientific publication, please cite:
 
-NCBI BLAST+ integrated into Galaxy.
-P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo
-bioRxiv DOI: http://dx.doi.org/10.1101/014043 (preprint)
+Cock, P.J.A. and Pritchard, L. (2014). Galaxy as a platform for identifying
+candidate pathogen effectors. Chapter 1 in "Plant-Pathogen Interactions:
+Methods and Protocols (Second Edition)"; P. Birch, J. Jones, and J.I. Bos, eds.
+Methods in Molecular Biology. Humana Press, Springer. ISBN 978-1-62703-985-7.
+http://www.springer.com/life+sciences/plant+sciences/book/978-1-62703-985-7
 
-You should also cite Galaxy, and the NCBI BLAST+ tools:
+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
 
-BLAST+: architecture and applications.
-C. Camacho et al. BMC Bioinformatics 2009, 10:421.
-DOI: http://dx.doi.org/10.1186/1471-2105-10-421
+Bendtsen, J.D., Nielsen, H., von Heijne, G., Brunak, S. (2004)
+Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340: 783–95.
+http://dx.doi.org/10.1016/j.jmb.2004.05.028
+
+Krogh, A., Larsson, B., von Heijne, G., Sonnhammer, E. (2001)
+Predicting transmembrane protein topology with a hidden Markov model:
+application to complete genomes. J Mol Biol 305: 567- 580.
+http://dx.doi.org/10.1006/jmbi.2000.4315
 
 
-Automated Installation
-======================
+Additional References
+=====================
+
+Kikuchi, T., Cotton, J.A., Dalzell, J.J., Hasegawa. K., et al. (2011)
+Genomic insights into the origin of parasitism in the emerging plant
+pathogen *Bursaphelenchus xylophilus*. PLoS Pathog 7: e1002219.
+http://dx.doi.org/10.1371/journal.ppat.1002219
 
-Installation via the Galaxy Tool Shed should take care of the dependencies
-on Galaxy tools including the NCBI BLAST+ wrappers and associated binaries.
+Jones, J.T., Kumar, A., Pylypenko, L.A., Thirugnanasambandam, A., et al. (2009)
+Identification and functional characterization of effectors in expressed
+sequence tags from various life cycle stages of the potato cyst nematode
+*Globodera pallida*. Mol Plant Pathol 10: 815–28.
+http://dx.doi.org/10.1111/j.1364-3703.2009.00585.x
+
 
-However, this workflow requires a current version of the NCBI nr protein
-BLAST database to be listed in ``blastdb_p.loc`` with the key ``nr`` (lower
-case).
+Dependencies
+============
+
+These dependencies should be resolved automatically via the Galaxy Tool Shed:
+
+* http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
+* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
+
+However, at the time of writing those Galaxy tools have their own
+dependencies required for this workflow which require manual
+installation (SignalP v3.0 and TMHMM v2.0).
 
 
 History
@@ -183,7 +102,13 @@
 ======= ======================================================================
 Version Changes
 ------- ----------------------------------------------------------------------
-v0.1.0  - Initial Tool Shed release, targetting NCBI BLAST+ 2.2.29
+v0.0.1  - Initial release to Tool Shed (May, 2013)
+        - Expanded README file to include example data
+v0.0.2  - Updated versions of the tools used, inclulding core Galaxy Filter
+          tool to avoid warning about new ``header_lines`` parameter.
+        - Added link to Tool Shed in the workflow annotation explaining there
+          is a README file with sample data, and a requested citation.
+v0.0.3  - Use MIT licence.
 ======= ======================================================================
 
 
@@ -192,20 +117,18 @@
 
 This workflow is under source code control here:
 
-https://github.com/peterjc/galaxy_blast/tree/master/workflows/blast_top_hit_species
+https://github.com/peterjc/pico_galaxy/tree/master/workflows/secreted_protein_workflow
 
 To prepare the tar-ball for uploading to the Tool Shed, I use this:
 
-    $ tar -cf blast_top_hit_species.tar.gz README.rst repository_dependencies.xml blast_top_hit_species.ga blast_top_hit_species.png N_abberans_piechart_mouseover.png
+    $ tar -cf secreted_protein_workflow.tar.gz README.rst repository_dependencies.xml secreted_protein_workflow.ga
 
 Check this,
 
-    $ tar -tzf blast_top_hit_species.tar.gz
+    $ tar -tzf secreted_protein_workflow.tar.gz 
     README.rst
     repository_dependencies.xml
-    blast_top_hit_species.ga
-    blast_top_hit_species.png
-    N_abberans_piechart_mouseover.png
+    secreted_protein_workflow.ga
 
 
 Licence (MIT)