diff tools/blast2go/blast2go.xml @ 8:e23b621eb7bb draft

Uploaded v0.0.9, embed citation, updated README

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/blast2go/blast2go.xml	Thu Mar 26 11:15:22 2015 -0400
@@ -0,0 +1,124 @@
+<tool id="blast2go" name="Blast2GO" version="0.0.9">
+    <description>Maps BLAST results to GO annotation terms</description>
+    <requirements>
+        <requirement type="package" version="2.5">b2g4pipe</requirement>
+    </requirements>
+    <command interpreter="python">
+        blast2go.py "${xml}" "${prop.fields.path}" "${tab}"
+    </command>
+    <stdio>
+        <!-- Wrapper ensures anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+    <inputs>
+        <param name="xml" type="data" format="blastxml" label="BLAST XML results" description="You must have run BLAST against a protein database such as the NCBI non-redundant (NR) database. Use BLASTX for nucleotide queries, BLASTP for protein queries." /> 
+        <param name="prop" type="select" label="Blast2GO settings" description="One or more configurations can be setup, such as using the Blast2GO team's server in Spain, or a local database.">
+             <options from_file="blast2go.loc">
+                 <column name="value" index="0"/>
+                 <column name="name" index="1"/>
+                 <column name="path" index="2"/>
+             </options>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="tab" format="tabular" label="Blast2GO ${prop.fields.name}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="xml" value="blastp_sample.xml" ftype="blastxml"/>
+            <param name="prop" value="Spain_2011_June"/>
+            <output name="tab" file="blastp_sample.blast2go.tabular" ftype="tabular"/>
+        </test>
+    </tests>
+    <help>
+.. class:: warningmark
+
+**Note**. Blast2GO may take a substantial amount of time, especially if
+running against the public server in Spain. For large input datasets it
+is advisable to allow overnight processing, or consider subdividing.
+
+-----
+
+**What it does**
+
+This runs b2g4Pipe v2.5, which is the command line (no GUI) version of
+Blast2GO designed for use in pipelines.
+
+It takes as input BLAST XML results against a protein database, typically
+the NCBI non-redundant (NR) database. This tool will accept concatenated
+BLAST XML files (although they are technically invalid XML), which is very
+useful if you have sub-divided your protein FASTA files and run BLAST on
+them in batches.
+
+The BLAST matches are used to assign Gene Ontology (GO) annotation terms
+to each query sequence.
+
+The output from this tool is a tabular file containing three columns, with
+the order taken from query order in the original BLAST XML file:
+
+====== ====================
+Column Description
+------ --------------------
+     1 ID of query sequence
+     2 GO term
+     3 GO description
+====== ====================
+
+Note that if no GO terms are assigned to a sequence (e.g. if it had no
+BLAST matches), then it will not be present in the output file.
+
+This tabular file is called an "Annotation File" in the Blast2GO GUI.
+If you download the tabular file, and rename it to use the extension
+".annot", then it can be opened with the Blast2GO GUI via the "File",
+"Load Annotation (.annot)" menu (keyboard shortcut ALT+L). You can
+then run some of the interactive analyses offered in the GUI tool.
+
+
+**Advanced Settings**
+
+Blast2GO has a properties setting file which includes which database
+server to connect to (e.g. the public server in Valencia, Spain, or a
+local server), as well as more advanced options such as thresholds and
+evidence code weights. To change these settings, your Galaxy administrator
+must create a new properties file, and add it to the drop down menu above.
+
+
+**References**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following papers:
+
+Peter Cock, Bjoern Gruening, 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
+
+S. Götz et al. (2008).
+High-throughput functional annotation and data mining with the Blast2GO suite.
+Nucleic Acids Res. 36(10):3420–3435.
+http://dx.doi.org/10.1093/nar/gkn176
+
+A. Conesa and S. Götz (2008).
+Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics.
+International Journal of Plant Genomics. 619832.
+http://dx.doi.org/10.1155/2008/619832
+
+A. Conesa et al. (2005).
+Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research.
+Bioinformatics 21:3674-3676.
+http://dx.doi.org/10.1093/bioinformatics/bti610
+
+See also http://www.blast2go.com/
+
+This wrapper is available to install into other Galaxy Instances via the Galaxy
+Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go
+
+    </help>
+    <citations>
+        <citation type="doi">10.7717/peerj.167</citation>
+        <citation type="doi">10.1093/nar/gkn176</citation>
+        <citation type="doi">10.1155/2008/619832</citation>
+        <citation type="doi">10.1093/bioinformatics/bti610</citation>
+    </citations>
+</tool>