# 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 @@
 <?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