| Previous changeset 0:c9699375fcf6 (2016-07-13) Next changeset 2:2b0210a098ba (2016-07-14) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm commit 2effed877a778e455c63a76e994a0f2bb8f4dba0 |
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modified:
glimmerHMM/glimmerhmm_predict.xml glimmerHMM/glimmerhmm_to_sequence.xml tool_conf.xml |
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removed:
readme.txt |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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> |
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| 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 |
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| @@ -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. - |