diff tools/protein_analysis/promoter2.xml @ 16:7de64c8b258d draft

Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub

--- a/tools/protein_analysis/promoter2.xml	Thu Apr 25 12:25:52 2013 -0400
+++ b/tools/protein_analysis/promoter2.xml	Wed Sep 18 06:16:58 2013 -0400
@@ -1,13 +1,15 @@
-<tool id="promoter2" name="Promoter 2.0" version="0.0.4">
+<tool id="promoter2" name="Promoter 2.0" version="0.0.6">
     <description>Find eukaryotic PolII promoters in DNA sequences</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <!-- Using 2000 per chunk so 4 threads each doing 500 is ideal -->
     <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
     <command interpreter="python">
         promoter2.py "\$NSLOTS" $fasta_file $tabular_file
+        ##I want the number of threads to be a Galaxy config option...
         ##Set the number of threads in the runner entry in universe_wsgi.ini
         ##which (on SGE at least) will set the $NSLOTS environment variable.
-        ##If the environment variable isn't set, get "", and defaults to one.
+        ##If the environment variable isn't set, get "", and the python wrapper
+        ##defaults to four threads.
     </command>
     <stdio>
         <!-- Anything other than zero is an error -->
@@ -41,10 +43,14 @@
 
 The input is a FASTA file of nucleotide sequences (e.g. upstream regions of your genes), and the output is tabular with five columns (one row per promoter):
 
- 1. Sequence identifier (first word of FASTA header)
- 2. Promoter position, e.g. 600
- 3. Promoter score, e.g. 1.063
- 4. Promoter likelihood, e.g. Highly likely prediction
+====== ==================================================
+Column Description
+------ --------------------------------------------------
+     1 Sequence identifier (first word of FASTA header)
+     2 Promoter position, e.g. 600
+     3 Promoter score, e.g. 1.063
+     4 Promoter likelihood, e.g. Highly likely prediction
+====== ==================================================
 
 The scores are classified very simply as follows:
 
@@ -61,12 +67,22 @@
 
 **References**
 
-Knudsen.
+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
+
+Steen Knudsen (1999).
 Promoter2.0: for the recognition of PolII promoter sequences.
-Bioinformatics, 15:356-61, 1999.
+Bioinformatics, 15:356-61.
 http://dx.doi.org/10.1093/bioinformatics/15.5.356
 
-http://www.cbs.dtu.dk/services/Promoter/output.php
+See also http://www.cbs.dtu.dk/services/Promoter/output.php
 
+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>
 </tool>