diff readme.md @ 0:c9699375fcf6 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.md	Wed Jul 13 10:55:48 2016 -0400
@@ -0,0 +1,82 @@
+Galaxy wrapper for GlimmerHMM
+=====================================
+
+This wrapper has been written in 2012 by Björn Grüning, and updated by Rémi Marenco in 2016.
+
+This is a wrapper for the command line tool of GlimmerHMM.
+https://ccb.jhu.edu/software/glimmerhmm/
+
+GlimmerHMM is a 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://ccb.jhu.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 $GALAXY_ROOT/config/tool_conf.xml file to make the tool available to Galaxy.
+For example:
+
+```xml
+<tool file="gene_prediction/tools/glimmerHMM/glimmerhmm_predict.xml" />
+<tool file="gene_prediction/tools/glimmerHMM/glimmerhmm_to_sequence.xml" />
+```
+
+You also need to use a trained organism by adding them as reference data in Galaxy:
+
+1. Add the *glimmer_hmm_trained_dir* data table to `tool_data_table_conf.xml` in `$GALAXY_ROOT/config/`:
+        
+    ```xml
+    <!-- glimmer_hmm trained_dir -->
+    <table name="glimmer_hmm_trained_dir" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/glimmer_hmm.loc" />
+    </table>
+    ```
+    
+2. Add the `glimmer_hmm.loc` file referencing your trained organism, in `tool-data`.
+    You have a sample [`glimmer_hmm.loc.sample`] available in the repository to help you configuring it properly
+3. Add your data in the chosen folder at step 2. You can get them from the GlimmerHMM tar, `$GLIMMERHMM/trained_dir`
+
+History
+=======
+
+- v2.0 - Update by Rémi Marenco to make it work without having to modify the wrapper + add ability to select the species
+- 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.