# HG changeset patch
# User rmarenco
# Date 1468523493 14400
# Node ID 4da91bb244dc1ce0aa9bf2d41afc7d203e347f2a
# Parent  c9699375fcf6a53e2db7f0f7b2e8ac8097da7d81
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 2effed877a778e455c63a76e994a0f2bb8f4dba0

diff -r c9699375fcf6 -r 4da91bb244dc glimmerHMM/glimmerhmm_predict.xml
--- a/glimmerHMM/glimmerhmm_predict.xml	Wed Jul 13 10:55:48 2016 -0400
+++ b/glimmerHMM/glimmerhmm_predict.xml	Thu Jul 14 15:11:33 2016 -0400
@@ -62,5 +62,7 @@
         ConsensusfromCH236920mapping  GlimmerHMM  CDS   15137   15205   .   -   0   ID=ConsensusfromCH236920mapping.cds2.2;
         ConsensusfromCH236920mapping  GlimmerHMM  mRNA  19910   24210   .   -   .   ID=ConsensusfromCH236920mapping.path1.gene3;Name=ConsensusfromCH236920mapping.path1.gene3
 
+
+
     </help>
 </tool>
diff -r c9699375fcf6 -r 4da91bb244dc glimmerHMM/glimmerhmm_to_sequence.xml
--- a/glimmerHMM/glimmerhmm_to_sequence.xml	Wed Jul 13 10:55:48 2016 -0400
+++ b/glimmerHMM/glimmerhmm_to_sequence.xml	Thu Jul 14 15:11:33 2016 -0400
@@ -1,13 +1,10 @@
 <tool id="glimmerhmm_to_sequence" name="GlimmerHMM to Sequence" version="0.1">
     <description>converter</description>
-    <command interpreter='python'>
-<![CDATA[
-    glimmerhmm_to_sequence.py
-        $glimmerhmm_input
-        $genome_input
-        $output
-        $to_protein
-]]>
+    <command interpreter='python'>glimmerhmm_to_sequence.py 
+    $glimmerhmm_input
+    $genome_input
+    $output
+    $to_protein
     </command>
     <inputs>
         <param name="genome_input" type="data" format="fasta" label="Genome Sequence" />
@@ -18,12 +15,10 @@
         <data name="output" format="fasta" />
     </outputs>
     <help>
-<![CDATA[
 
 **What it does**
 
 It converts the GlimmerHMM GFF output to a Fasta File.
 
-]]>
     </help>
 </tool>
diff -r c9699375fcf6 -r 4da91bb244dc readme.txt
--- a/readme.txt	Wed Jul 13 10:55:48 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,65 +0,0 @@
-Galaxy wrapper for RepeatMasker
-=====================================
-
-This wrapper is copyright 2012 by Björn Grüning.
-
-This is a wrapper for the command line tool of GlimmerHMM.
-http://www.cbcb.umd.edu/software/GlimmerHMM/
-
-GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM). Although the gene finder conforms to the overall mathematical framework of a GHMM,
-additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes
-Interpolated Markov Models for the coding and noncoding models.
-Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons (initial, internal, final, and single).
-
-Majoros, W.H., Pertea, M., and Salzberg, S.L. TigrScan and GlimmerHMM: two open-source ab initio eukaryotic gene-finders Bioinformatics 20 2878-2879.
-Pertea, M. and S. L. Salzberg (2002). "Computational gene finding in plants." Plant Molecular Biology 48(1-2): 39-48.
-The Arabidopsis Genome Initiative, (2000) "Analysis of the genome sequence of the flowering plant Arabidopsis thaliana", Nature. Dec 14; 408(6814):796-815.
-Pertea, M., S. L. Salzberg, et al. (2000). "Finding genes in Plasmodium falciparum." Nature 404(6773): 34; discussion 34-5.
-Salzberg, S. L., M. Pertea, et al. (1999). "Interpolated Markov models for eukaryotic gene finding." Genomics 59(1): 24-31. 
-
-
-Installation
-============
-
-To install Glimmer3, please download GlimmerHMM from 
-
-ftp://ftp.cbcb.umd.edu/pub/software/glimmerhmm/
-
-and follow the installation instructions.
-To extract the glimmerHMM predicted genes, the GFF Parser from Brad Chapman (ttp://github.com/chapmanb/bcbb/tree/master/gff) was used and is included.
-
-To install the wrapper copy the glimmerHMM folder in the galaxy tools
-folder and modify the tools_conf.xml file to make the tool available to Galaxy.
-For example:
-
-<tool file="gene_prediction/tools/glimmerHMM/glimmerhmm_predict.xml" />
-<tool file="gene_prediction/tools/glimmerHMM/glimmerhmm_to_sequence.xml" />
-
-
-History
-=======
-
-v0.1 - Initial public release
-
-
-Wrapper Licence (MIT/BSD style)
-===============================
-
-Permission to use, copy, modify, and distribute this software and its
-documentation with or without modifications and for any purpose and
-without fee is hereby granted, provided that any copyright notices
-appear in all copies and that both those copyright notices and this
-permission notice appear in supporting documentation, and that the
-names of the contributors or copyright holders not be used in
-advertising or publicity pertaining to distribution of the software
-without specific prior permission.
-
-THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
-WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
-CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
-OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
-OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
-OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
-OR PERFORMANCE OF THIS SOFTWARE.
-
diff -r c9699375fcf6 -r 4da91bb244dc tool_conf.xml