# HG changeset patch
# User yhoogstrate
# Date 1427613613 14400
# Node ID 4e00cc7b97e597f86d2bed4845f2a53efe43bb24
# Parent  c9f0f918bef6390755affd28f0829c14a1284078
Uploaded

diff -r c9f0f918bef6 -r 4e00cc7b97e5 flaimapper.xml
--- a/flaimapper.xml	Sun Mar 29 02:54:20 2015 -0400
+++ b/flaimapper.xml	Sun Mar 29 03:20:13 2015 -0400
@@ -26,7 +26,7 @@
 	</stdio>
 	
 	<inputs>
-		<param name="alignments" type="data" format="bam,sam" label="Alignment file(s)" help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files in the series must be in THE SAME format." multiple="true" />
+		<param name="alignments" type="data" format="bam" label="Alignment file(s)" help="Aligned small RNA-Seq reads which may not be fragmented. In case you add multiple BAM files, FlaiMapper will simply concatenate the data and perform one single analysis on the entire set of alignments." multiple="true" />
 		
 		<param name="mask" type="data" format="gtf,gff,gff3" label="small ncRNA Annotation (gtf)" help="" />
 			
@@ -67,28 +67,54 @@
 
 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:
+
+Input
+-----
+
+Alignments
+**********
+
+Aligned reads from small RNA-Seq experiments have to be provided in the BAM format.
+In case you add multiple BAM files, FlaiMapper will simply concatenate the data and perform one single analysis on the entire set of alignments.
+
+Mask File
+*********
+
+There are two strategies to analyze using FlaiMapper:
+
+- Relative to mature ncRNA sequences
+- Relative to chromosomes
+
+Therefore FlaiMapper requires a list of ncRNA annotations relative to the used reference genome for the alignment files. These ncRNA locations within the sequences provided in the FASTA file (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
 
+If you are making use of a ncRNA database that has no GTF file available you can make use of the galaxy tool **flaimapper-gtf-from-fasta** to create one.
+
+
+You can access **ncRNAdb09** GTF file at the following URL:
+https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.gtf *(mask file)*
+
+Fasta sequence
+**************
+
 The reference sequence should be provided in FASTA format.
 
-You can access **ncRNAdb09** at the following URLs:
-https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.gtf *(mask file)*
+You can access **ncRNAdb09** FASTA file at the following URL:
 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.fa *(reference file)*
 
-Therefore you need bam files aligned to the same reference. We have made
-the following available:
+Example- and reference data
+***************************
+
+To align reads to ncRNA you need aligner specific indexed version of the reference. We have made
+the following available for ncRNAdb09:
 
  - **Tophat1**: https://github.com/yhoogstrate/flaimapper/blob/master/share/annotations/ncRNA_annotation/ncrnadb09.bt2.tar.gz
  - **Tophat2**: https://github.com/yhoogstrate/flaimapper/blob/master/share/annotations/ncRNA_annotation/ncrnadb09.bt2.tar.gz
 
-If you want to test flaimapper with example data you can obtain several
-alignment files from this following directory tree:
+If you want to test FlaiMapper with example data you can obtain several
+alignment files from the following directory tree:
 
 https://github.com/yhoogstrate/flaimapper/tree/master/share/small_RNA-seq_alignments