# HG changeset patch
# User erasmus-medical-center
# Date 1493377548 14400
# Node ID 0ea90514e0a042f8f188f6a4d6216989e80ec284
# Parent  c143e7e1fdbf5ff416d78401dd3ece9c8c05ffaf
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit beb30713f9b8510c22f46d94cb58c92cf26c799c

diff -r c143e7e1fdbf -r 0ea90514e0a0 flaimapper.xml
--- a/flaimapper.xml	Mon Jan 23 03:13:40 2017 -0500
+++ b/flaimapper.xml	Fri Apr 28 07:05:48 2017 -0400
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="flaimapper" name="FlaiMapper" version="2.3.4-0">
+<tool id="flaimapper" name="FlaiMapper" version="2.4.0-0">
     <description>detects small ncRNA derived fragments in small RNA-Seq data</description>
     <requirements>
-        <requirement type="package" version="2.3.4">flaimapper</requirement>
+        <requirement type="package" version="2.4.0">flaimapper</requirement>
     </requirements>
     
     <version_command>flaimapper --version 2&gt;&amp;1 | head -n 1</version_command>
@@ -42,16 +42,17 @@
             
             <when value="1">
                 <param name="fasta" type="data" format="fasta" optional="true"
-                       label="(Optional) Genome reference in FASTA format that corresponds to the reference genome or RNA database" help="By selecting this file, sequences will be provided in the corresponding column in the output file" argument="-r" />
+                       label="(Optional) Genome reference in FASTA format that corresponds to the reference genome or RNA database"
+                       help="By selecting this file, sequences will be provided in the corresponding column in the output file" argument="-r" />
             </when>
             
             <when value="2">
                 <param name="offset5p" type="integer" value="4"
-                       label="5' offset added to the exon-type GTF entry"
-                       help="Exon-type entries are often used to measure expression. Because of the small size of the fragments it may be desired to use an offset." argument="--offset5p" />
+                       label="Add 5'-offset to exon-type entry in GTF output file"
+                       help="Exon-type entries are often used to measure expression. Because of the small size of the fragments it may be desired to add an offset to allow less stringent read counting." argument="--offset5p" />
                 <param name="offset3p" type="integer" value="4"
-                       label="3' offset added to the exon-type GTF entry"
-                       help="Exon-type entries are often used to measure expression. Because of the small size of the fragments it may be desired to use an offset." argument="--offset3p" />
+                       label="Add 3'-offset to exon-type entry in GTF output file"
+                       help="Exon-type entries are often used to measure expression. Because of the small size of the fragments it may be desired to add an offset to allow less stringent read counting." argument="--offset3p" />
             </when>
         </conditional>
         
diff -r c143e7e1fdbf -r 0ea90514e0a0 test-data/snord81.flaimapper.duck-15.gtf
--- a/test-data/snord81.flaimapper.duck-15.gtf	Mon Jan 23 03:13:40 2017 -0500
+++ b/test-data/snord81.flaimapper.duck-15.gtf	Fri Apr 28 07:05:48 2017 -0400
@@ -1,4 +1,4 @@
-HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.3.4	sncdRNA	47	68	171	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001"
-HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.3.4	exon	43	72	171	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001"
-HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.3.4	sncdRNA	15	37	99	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002"
-HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.3.4	exon	11	41	99	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002"
+HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.4.0	sncdRNA	47	68	171	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001"
+HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.4.0	exon	43	72	171	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001"
+HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.4.0	sncdRNA	15	37	99	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002"
+HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.4.0	exon	11	41	99	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002"
diff -r c143e7e1fdbf -r 0ea90514e0a0 test-data/snord81.flaimapper.gtf
--- a/test-data/snord81.flaimapper.gtf	Mon Jan 23 03:13:40 2017 -0500
+++ b/test-data/snord81.flaimapper.gtf	Fri Apr 28 07:05:48 2017 -0400
@@ -1,6 +1,6 @@
-HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.3.4	sncdRNA	47	68	171	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001"
-HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.3.4	exon	43	72	171	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001"
-HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.3.4	sncdRNA	15	37	99	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002"
-HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.3.4	exon	11	41	99	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002"
-HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.3.4	sncdRNA	55	80	82	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000003"
-HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.3.4	exon	51	84	82	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000003"
+HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.4.0	sncdRNA	47	68	171	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001"
+HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.4.0	exon	43	72	171	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001"
+HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.4.0	sncdRNA	15	37	99	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002"
+HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.4.0	exon	11	41	99	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002"
+HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.4.0	sncdRNA	55	80	82	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000003"
+HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.4.0	exon	51	84	82	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000003"
diff -r c143e7e1fdbf -r 0ea90514e0a0 test-data/snord81.flaimapper.offsets_5_5.gtf
--- a/test-data/snord81.flaimapper.offsets_5_5.gtf	Mon Jan 23 03:13:40 2017 -0500
+++ b/test-data/snord81.flaimapper.offsets_5_5.gtf	Fri Apr 28 07:05:48 2017 -0400
@@ -1,6 +1,6 @@
-HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.3.4	sncdRNA	47	68	171	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001"
-HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.3.4	exon	42	73	171	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001"
-HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.3.4	sncdRNA	15	37	99	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002"
-HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.3.4	exon	10	42	99	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002"
-HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.3.4	sncdRNA	55	80	82	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000003"
-HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.3.4	exon	50	85	82	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000003"
+HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.4.0	sncdRNA	47	68	171	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001"
+HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.4.0	exon	42	73	171	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000001"
+HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.4.0	sncdRNA	15	37	99	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002"
+HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.4.0	exon	10	42	99	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000002"
+HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.4.0	sncdRNA	55	80	82	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000003"
+HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19	flaimapper-v2.4.0	exon	50	85	82	.	.	gene_id "FM_HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_000000000003"
diff -r c143e7e1fdbf -r 0ea90514e0a0 test-data/test_genomic_flaimapper_output.gtf
--- a/test-data/test_genomic_flaimapper_output.gtf	Mon Jan 23 03:13:40 2017 -0500
+++ b/test-data/test_genomic_flaimapper_output.gtf	Fri Apr 28 07:05:48 2017 -0400
@@ -1,12 +1,12 @@
-chr1	flaimapper-v2.3.4	sncdRNA	261	290	20	.	.	gene_id "FM_chr1_000000000001"
-chr1	flaimapper-v2.3.4	exon	257	294	20	.	.	gene_id "FM_chr1_000000000001"
-chr1	flaimapper-v2.3.4	sncdRNA	221	250	19	.	.	gene_id "FM_chr1_000000000002"
-chr1	flaimapper-v2.3.4	exon	217	254	19	.	.	gene_id "FM_chr1_000000000002"
-chr1	flaimapper-v2.3.4	sncdRNA	401	430	20	.	.	gene_id "FM_chr1_000000000001"
-chr1	flaimapper-v2.3.4	exon	397	434	20	.	.	gene_id "FM_chr1_000000000001"
-chr22	flaimapper-v2.3.4	sncdRNA	101	150	20	.	.	gene_id "FM_chr22_000000000001"
-chr22	flaimapper-v2.3.4	exon	97	154	20	.	.	gene_id "FM_chr22_000000000001"
-chr22	flaimapper-v2.3.4	sncdRNA	371	400	20	.	.	gene_id "FM_chr22_000000000001"
-chr22	flaimapper-v2.3.4	exon	367	404	20	.	.	gene_id "FM_chr22_000000000001"
-chrY	flaimapper-v2.3.4	sncdRNA	1	30	19	.	.	gene_id "FM_chrY_000000000001"
-chrY	flaimapper-v2.3.4	exon	1	34	19	.	.	gene_id "FM_chrY_000000000001"
+chr1	flaimapper-v2.4.0	sncdRNA	261	290	20	.	.	gene_id "FM_chr1_000000000001"
+chr1	flaimapper-v2.4.0	exon	257	294	20	.	.	gene_id "FM_chr1_000000000001"
+chr1	flaimapper-v2.4.0	sncdRNA	221	250	19	.	.	gene_id "FM_chr1_000000000002"
+chr1	flaimapper-v2.4.0	exon	217	254	19	.	.	gene_id "FM_chr1_000000000002"
+chr1	flaimapper-v2.4.0	sncdRNA	401	430	20	.	.	gene_id "FM_chr1_000000000001"
+chr1	flaimapper-v2.4.0	exon	397	434	20	.	.	gene_id "FM_chr1_000000000001"
+chr22	flaimapper-v2.4.0	sncdRNA	101	150	20	.	.	gene_id "FM_chr22_000000000001"
+chr22	flaimapper-v2.4.0	exon	97	154	20	.	.	gene_id "FM_chr22_000000000001"
+chr22	flaimapper-v2.4.0	sncdRNA	371	400	20	.	.	gene_id "FM_chr22_000000000001"
+chr22	flaimapper-v2.4.0	exon	367	404	20	.	.	gene_id "FM_chr22_000000000001"
+chrY	flaimapper-v2.4.0	sncdRNA	1	30	19	.	.	gene_id "FM_chrY_000000000001"
+chrY	flaimapper-v2.4.0	exon	1	34	19	.	.	gene_id "FM_chrY_000000000001"