# HG changeset patch # User yhoogstrate # Date 1426845666 14400 # Node ID fb1537d0462531f8353cf6be0087e061dc825e0b # Parent 5e677aafc3a1a9a69b9f4abc1441b2b6f593bed5 Uploaded diff -r 5e677aafc3a1 -r fb1537d04625 flaimapper.xml --- 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 @@ - + Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper. pysam @@ -41,10 +41,75 @@ - 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 + + + 10.1093/bioinformatics/btu696 + \ No newline at end of file