diff tools/ncbi_blast_plus/blast2go.xml @ 0:cd52c931b325

Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/ncbi_blast_plus/blast2go.xml	Tue Jun 07 16:28:31 2011 -0400
@@ -0,0 +1,75 @@
+<tool id="blast2go" name="Blast2GO" version="0.0.1">
+    <description>Maps BLAST results to GO annotation terms</description>
+    <command interpreter="python">
+        blast2go.py $xml ${prop.fields.path} $tab
+    </command>
+    <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>
+    <requirements>
+    </requirements>
+    <tests>
+    </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, 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. 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 and description 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.
+
+**References**
+
+S. Götz et al.
+High-throughput functional annotation and data mining with the Blast2GO suite.
+Nucleic Acids Res. 36(10):3420–3435, 2008.
+http://dx.doi.org/10.1093/nar/gkn176
+
+A. Conesa and S. Götz.
+Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics.
+Int. J. Plant Genomics. 619832, 2008.
+http://dx.doi.org/10.1155/2008/619832
+
+A. Conesa et al.
+Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research.
+Bioinformatics 21:3674-3676, 2005.
+http://dx.doi.org/10.1093/bioinformatics/bti610
+
+http://www.blast2go.org/
+
+    </help>
+</tool>