Mercurial > repos > yhoogstrate > flaimapper
changeset 14:fb1537d04625 draft
Uploaded
author | yhoogstrate |
---|---|
date | Fri, 20 Mar 2015 06:01:06 -0400 |
parents | 5e677aafc3a1 |
children | ae3e699a4ae5 |
files | flaimapper.xml |
diffstat | 1 files changed, 71 insertions(+), 6 deletions(-) [+] |
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--- a/flaimapper.xml Thu Mar 19 11:40:56 2015 -0400 +++ b/flaimapper.xml Fri Mar 20 06:01:06 2015 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="flaimapper" name="FlaiMapper" version="1.1.2.a"> +<tool id="flaimapper" name="FlaiMapper" version="1.1.2.b"> <description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description> <requirements> <requirement type="package" version="0.8.1">pysam</requirement><!-- pysam 0.7.7 ABSOLUTELY CRASHES !!! --> @@ -41,10 +41,75 @@ </outputs> <help> - You must have 'easy_install' installed. - - FlaiMapper: computational annotation of small ncRNA derived fragments using RNA-seq high throughput data - - doi:10.1093/bioinformatics/btu696 +FlaiMapper wrapper for Galaxy +============================= + +https://github.com/yhoogstrate/flaimapper +http://www.ncbi.nlm.nih.gov/pubmed/25338717 +http://dx.doi.org/10.1093/bioinformatics/btu696 + +Fragment Location Annotation Identification Mapper + +FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data. + +Input formats +------------- +Alignments should be provided in BAM format. +Gene (MASK) regions should be provided in the GFF/GTF format: + +- http://genome.ucsc.edu/FAQ/FAQformat.html#format3 +- http://www.ensembl.org/info/website/upload/gff.html + +The reference sequence should be provided in FASTSA format. + +Installation +------------ + +The wrapper makes use of easy_install to install a python egg. Please +ensure you have easy_install installed. + +License +------- + +**flaimapper** and **wrapper**: + +GPL (>=3) + +**pysam**: + +The MIT License (>=3) + +Contact +------- + +The tool wrapper has been written by Youri Hoogstrate from the Erasmus +Medical Center (Rotterdam, Netherlands). + + +Development +----------- + +* Repository-Maintainer: Youri Hoogstrate +* Repository-Developers: Youri Hoogstrate + +* Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools + +The tool wrapper has been written by Youri Hoogstrate from the Erasmus +Medical Center (Rotterdam, Netherlands). + +References +---------- +**FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.** + +*Hoogstrat* - Bioinformatics. 2014 Apr 1;30(7):923-30. + +*Youri Hoogstrate, Guido Jenster, and Elena S. Martens-Uzunova* - Bioinformatics (2015) 31 (5): 665-673 + +- http://www.ncbi.nlm.nih.gov/pubmed/25338717 +- http://dx.doi.org/10.1093/bioinformatics/btu696 </help> + + <citations> + <citation type="doi">10.1093/bioinformatics/btu696</citation> + </citations> </tool> \ No newline at end of file