# HG changeset patch
# User peterjc
# Date 1367515978 14400
# Node ID af3174637834b211db599e703bd96191b790bf5c
# Parent  1d5486a02bc44a9827952bd2b1f680e017272b0e
Uploaded v0.2.5 preview 1, adding links to Tool Shed entry

diff -r 1d5486a02bc4 -r af3174637834 tools/protein_analysis/README
--- a/tools/protein_analysis/README	Thu Apr 25 12:25:23 2013 -0400
+++ b/tools/protein_analysis/README	Thu May 02 13:32:58 2013 -0400
@@ -19,6 +19,9 @@
 Contributions/revisions copyright 2011 Konrad Paszkiewicz. All rights reserved.
 See the included LICENCE file for details (an MIT style open source licence).
 
+The wrappers are available from the Galaxy Tool Shed
+http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp 
+
 
 Requirements
 ============
@@ -143,6 +146,7 @@
 v0.2.2 - Include missing test files.
 v0.2.3 - Added unit tests for WoLF PSORT.
 v0.2.4 - Added unit tests for Promoter 2
+v0.2.5 - Link to Tool Shed added to help text and this documentation.
 
 
 Developers
diff -r 1d5486a02bc4 -r af3174637834 tools/protein_analysis/promoter2.xml
--- a/tools/protein_analysis/promoter2.xml	Thu Apr 25 12:25:23 2013 -0400
+++ b/tools/protein_analysis/promoter2.xml	Thu May 02 13:32:58 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="promoter2" name="Promoter 2.0" version="0.0.4">
+<tool id="promoter2" name="Promoter 2.0" version="0.0.5">
     <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 -->
@@ -68,5 +68,7 @@
 
 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>
diff -r 1d5486a02bc4 -r af3174637834 tools/protein_analysis/psortb.xml
--- a/tools/protein_analysis/psortb.xml	Thu Apr 25 12:25:23 2013 -0400
+++ b/tools/protein_analysis/psortb.xml	Thu May 02 13:32:58 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="Psortb" name="psortb" version="0.0.1">
+<tool id="Psortb" name="psortb" version="0.0.2">
   <description>Determines sub-cellular localisation of bacterial/archaeal protein sequences</description>
   <!-- If job splitting is enabled, break up the query file into parts -->
   <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal -->
@@ -85,5 +85,7 @@
 
 http://www.psort.org/documentation/index.html
 
+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>
diff -r 1d5486a02bc4 -r af3174637834 tools/protein_analysis/rxlr_motifs.xml
--- a/tools/protein_analysis/rxlr_motifs.xml	Thu Apr 25 12:25:23 2013 -0400
+++ b/tools/protein_analysis/rxlr_motifs.xml	Thu May 02 13:32:58 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="rxlr_motifs" name="RXLR Motifs" version="0.0.6">
+<tool id="rxlr_motifs" name="RXLR Motifs" version="0.0.7">
     <description>Find RXLR Effectors of Plant Pathogenic Oomycetes</description>
     <command interpreter="python">
       rxlr_motifs.py $fasta_file 8 $model $tabular_file
@@ -150,5 +150,7 @@
 Protein Engineering, 10:1-6, 1997.
 http://dx.doi.org/10.1093/protein/10.1.1
 
+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>
diff -r 1d5486a02bc4 -r af3174637834 tools/protein_analysis/signalp3.xml
--- a/tools/protein_analysis/signalp3.xml	Thu Apr 25 12:25:23 2013 -0400
+++ b/tools/protein_analysis/signalp3.xml	Thu May 02 13:32:58 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="signalp3" name="SignalP 3.0" version="0.0.11">
+<tool id="signalp3" name="SignalP 3.0" version="0.0.12">
     <description>Find signal peptides in protein sequences</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal -->
@@ -185,5 +185,7 @@
 
 http://www.cbs.dtu.dk/services/SignalP-3.0/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>
diff -r 1d5486a02bc4 -r af3174637834 tools/protein_analysis/tmhmm2.xml
--- a/tools/protein_analysis/tmhmm2.xml	Thu Apr 25 12:25:23 2013 -0400
+++ b/tools/protein_analysis/tmhmm2.xml	Thu May 02 13:32:58 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="tmhmm2" name="TMHMM 2.0" version="0.0.10">
+<tool id="tmhmm2" name="TMHMM 2.0" version="0.0.11">
     <description>Find transmembrane domains in protein sequences</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal -->
@@ -106,5 +106,7 @@
 
 http://www.cbs.dtu.dk/services/TMHMM/
 
+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>
diff -r 1d5486a02bc4 -r af3174637834 tools/protein_analysis/wolf_psort.xml
--- a/tools/protein_analysis/wolf_psort.xml	Thu Apr 25 12:25:23 2013 -0400
+++ b/tools/protein_analysis/wolf_psort.xml	Thu May 02 13:32:58 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="wolf_psort" name="WoLF PSORT" version="0.0.4">
+<tool id="wolf_psort" name="WoLF PSORT" version="0.0.5">
     <description>Eukaryote protein subcellular localization prediction</description>
     <command interpreter="python">
       wolf_psort.py $organism 8 $fasta_file $tabular_file
@@ -130,5 +130,7 @@
 
 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>
 </tool>