# HG changeset patch
# User erasmus-medical-center
# Date 1502896071 14400
# Node ID 4f22bd6127542948f4b1a66a525a133e617145c9
# Parent  0ea90514e0a042f8f188f6a4d6216989e80ec284
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad

diff -r 0ea90514e0a0 -r 4f22bd612754 flaimapper.xml
--- a/flaimapper.xml	Fri Apr 28 07:05:48 2017 -0400
+++ b/flaimapper.xml	Wed Aug 16 11:07:51 2017 -0400
@@ -1,12 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="flaimapper" name="FlaiMapper" version="2.4.0-0">
+<tool id="flaimapper" name="FlaiMapper" version="2.5.0-0">
     <description>detects small ncRNA derived fragments in small RNA-Seq data</description>
     <requirements>
-        <requirement type="package" version="2.4.0">flaimapper</requirement>
+        <requirement type="package" version="2.5.0">flaimapper</requirement>
     </requirements>
-    
-    <version_command>flaimapper --version 2&gt;&amp;1 | head -n 1</version_command>
-    
+
+    <version_command><![CDATA[ flaimapper --version 2>&1 | head -n 1 ]]></version_command>
+
     <command detect_errors="exit_code"><![CDATA[
         flaimapper
             -v
@@ -28,24 +28,24 @@
 
             '${alignment}'
     ]]></command>
-    
+
     <inputs>
         <param name="alignment" type="data" format="bam" multiple="false"
                label="Alignment file"
                help="Aligned small RNA-Seq reads must be single end and should not be fragmented in the library preparation" />
-        
+
         <conditional name="output_select">
             <param name="output_format" type="select" label="Output format" argument="-f">
                 <option value="1">Tabular</option>
                 <option value="2">GTF</option>
             </param>
-            
+
             <when value="1">
                 <param name="fasta" type="data" format="fasta" optional="true"
                        label="(Optional) Genome reference in FASTA format that corresponds to the reference genome or RNA database"
                        help="By selecting this file, sequences will be provided in the corresponding column in the output file" argument="-r" />
             </when>
-            
+
             <when value="2">
                 <param name="offset5p" type="integer" value="4"
                        label="Add 5'-offset to exon-type entry in GTF output file"
@@ -55,12 +55,12 @@
                        help="Exon-type entries are often used to measure expression. Because of the small size of the fragments it may be desired to add an offset to allow less stringent read counting." argument="--offset3p" />
             </when>
         </conditional>
-        
+
         <param name="parameters" type="data" format="txt,tabular" optional="true"
                label="(Optional) Custom parameters file" help="" argument="-p" />
-        
+
     </inputs>
-    
+
     <outputs>
         <data format="tabular" name="output"
               label="${tool.name} on $on_string">
@@ -70,68 +70,72 @@
             </change_format>
         </data>
     </outputs>
-    
+
     <tests>
         <!-- tabular -->
-        <test><!-- Testing "ncRNAdb09 alignment"-type analysis -->
+        <!-- Testing "ncRNAdb09 alignment"-type analysis -->
+        <test>
             <param name="alignment" value="snord81.bam" ftype="bam" />
             <param name="fasta" value="snord81.fa" ftype="fasta" />
             <param name="output_format" value="1" />
-            
+
             <output name="output" file="snord81.flaimapper.txt" />
         </test>
         <test>
             <param name="alignment" value="snord81.bam" ftype="bam" />
             <param name="output_format" value="1" />
-            
+
             <output name="output" file="snord81.flaimapper.no-seq.txt" />
         </test>
-        <test><!-- Testing "Full genome alignment"-type analysis -->
+        <!-- Testing "Full genome alignment"-type analysis -->
+        <test>
             <param name="alignment" value="test_genomic_alignment.bam" ftype="bam" />
             <param name="fasta" value="test_genomic_all_chromosomes.fa" ftype="fasta" />
             <param name="output_format" value="1" />
-            
+
             <output name="output" file="test_genomic_flaimapper_output.txt" />
         </test>
         <test>
             <param name="alignment" value="test_genomic_alignment.bam" ftype="bam" />
             <param name="output_format" value="1" />
-            
+
             <output name="output" file="test_genomic_flaimapper_output.no-seq.txt" />
         </test>
-        
+
         <!-- GTF -->
-        <test><!-- Testing "ncRNAdb09 alignment"-type analysis -->
+        <!-- Testing "ncRNAdb09 alignment"-type analysis -->
+        <test>
             <param name="alignment" value="snord81.bam" ftype="bam" />
             <param name="output_format" value="2" />
-            
+
             <output name="output" file="snord81.flaimapper.gtf" />
         </test>
-        <test><!-- Testing "Full genome alignment"-type analysis -->
+        <!-- Testing "Full genome alignment"-type analysis -->
+        <test>
             <param name="alignment" value="test_genomic_alignment.bam" ftype="bam" />
             <param name="output_format" value="2" />
-            
+
             <output name="output" file="test_genomic_flaimapper_output.gtf" />
         </test>
-        
+
         <!-- test custom parameters -->
         <test>
             <param name="alignment" value="snord81.bam" ftype="bam" />
             <param name="output_format" value="2" />
             <param name="offset5p" value="5" />
             <param name="offset3p" value="5" />
-            
+
             <output name="output" file="snord81.flaimapper.offsets_5_5.gtf" />
         </test>
         <test>
             <param name="alignment" value="snord81.bam" ftype="bam" />
             <param name="output_format" value="2" />
             <param name="parameters" value="filter-parameters.duck.15.txt"/>
-            
+
             <output name="output" file="snord81.flaimapper.duck-15.gtf" />
         </test>
     </tests>
-    
+
     <help><![CDATA[
 FlaiMapper wrapper for Galaxy
 =============================
@@ -171,8 +175,8 @@
 
 https://github.com/yhoogstrate/flaimapper
     ]]></help>
-    
+
     <citations>
         <citation type="doi">10.1093/bioinformatics/btu696</citation>
     </citations>
-</tool>
\ No newline at end of file
+</tool>
diff -r 0ea90514e0a0 -r 4f22bd612754 test-data/snord81.flaimapper.duck-15.gtf
--- a/test-data/snord81.flaimapper.duck-15.gtf	Fri Apr 28 07:05:48 2017 -0400
+++ b/test-data/snord81.flaimapper.duck-15.gtf	Wed Aug 16 11:07:51 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-v2.4.0	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-v2.5.0	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-v2.5.0	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-v2.5.0	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-v2.5.0	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 0ea90514e0a0 -r 4f22bd612754 test-data/snord81.flaimapper.gtf
--- a/test-data/snord81.flaimapper.gtf	Fri Apr 28 07:05:48 2017 -0400
+++ b/test-data/snord81.flaimapper.gtf	Wed Aug 16 11:07:51 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-v2.4.0	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"
+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-v2.5.0	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-v2.5.0	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-v2.5.0	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-v2.5.0	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-v2.5.0	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-v2.5.0	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 0ea90514e0a0 -r 4f22bd612754 test-data/snord81.flaimapper.offsets_5_5.gtf
--- a/test-data/snord81.flaimapper.offsets_5_5.gtf	Fri Apr 28 07:05:48 2017 -0400
+++ b/test-data/snord81.flaimapper.offsets_5_5.gtf	Wed Aug 16 11:07:51 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-v2.4.0	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"
+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-v2.5.0	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-v2.5.0	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-v2.5.0	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-v2.5.0	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-v2.5.0	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-v2.5.0	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 0ea90514e0a0 -r 4f22bd612754 test-data/test_genomic_flaimapper_output.gtf
--- a/test-data/test_genomic_flaimapper_output.gtf	Fri Apr 28 07:05:48 2017 -0400
+++ b/test-data/test_genomic_flaimapper_output.gtf	Wed Aug 16 11:07:51 2017 -0400
@@ -1,12 +1,12 @@
-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"
+chr1	flaimapper-v2.5.0	sncdRNA	261	290	20	.	.	gene_id "FM_chr1_000000000001"
+chr1	flaimapper-v2.5.0	exon	257	294	20	.	.	gene_id "FM_chr1_000000000001"
+chr1	flaimapper-v2.5.0	sncdRNA	221	250	19	.	.	gene_id "FM_chr1_000000000002"
+chr1	flaimapper-v2.5.0	exon	217	254	19	.	.	gene_id "FM_chr1_000000000002"
+chr1	flaimapper-v2.5.0	sncdRNA	401	430	20	.	.	gene_id "FM_chr1_000000000003"
+chr1	flaimapper-v2.5.0	exon	397	434	20	.	.	gene_id "FM_chr1_000000000003"
+chr22	flaimapper-v2.5.0	sncdRNA	101	150	20	.	.	gene_id "FM_chr22_000000000001"
+chr22	flaimapper-v2.5.0	exon	97	154	20	.	.	gene_id "FM_chr22_000000000001"
+chr22	flaimapper-v2.5.0	sncdRNA	371	400	20	.	.	gene_id "FM_chr22_000000000002"
+chr22	flaimapper-v2.5.0	exon	367	404	20	.	.	gene_id "FM_chr22_000000000002"
+chrY	flaimapper-v2.5.0	sncdRNA	1	30	19	.	.	gene_id "FM_chrY_000000000001"
+chrY	flaimapper-v2.5.0	exon	1	34	19	.	.	gene_id "FM_chrY_000000000001"
diff -r 0ea90514e0a0 -r 4f22bd612754 test-data/test_genomic_flaimapper_output.no-seq.txt
--- a/test-data/test_genomic_flaimapper_output.no-seq.txt	Fri Apr 28 07:05:48 2017 -0400
+++ b/test-data/test_genomic_flaimapper_output.no-seq.txt	Wed Aug 16 11:07:51 2017 -0400
@@ -1,7 +1,7 @@
 Fragment	Size	Reference sequence	Start	End	Precursor	Start in precursor	End in precursor	Sequence	Corresponding-reads (start)	Corresponding-reads (end)	Corresponding-reads (total)
 FM_chr1_000000000001	30	chr1	260	289	chr1	56	85		10	10	20
 FM_chr1_000000000002	30	chr1	220	249	chr1	16	45		10	9	19
-FM_chr1_000000000001	30	chr1	400	429	chr1	16	45		10	10	20
+FM_chr1_000000000003	30	chr1	400	429	chr1	16	45		10	10	20
 FM_chr22_000000000001	50	chr22	100	149	chr22	16	65		10	10	20
-FM_chr22_000000000001	30	chr22	370	399	chr22	16	45		10	10	20
+FM_chr22_000000000002	30	chr22	370	399	chr22	16	45		10	10	20
 FM_chrY_000000000001	30	chrY	0	29	chrY	0	29		10	9	19
diff -r 0ea90514e0a0 -r 4f22bd612754 test-data/test_genomic_flaimapper_output.txt
--- a/test-data/test_genomic_flaimapper_output.txt	Fri Apr 28 07:05:48 2017 -0400
+++ b/test-data/test_genomic_flaimapper_output.txt	Wed Aug 16 11:07:51 2017 -0400
@@ -1,7 +1,7 @@
 Fragment	Size	Reference sequence	Start	End	Precursor	Start in precursor	End in precursor	Sequence (no fasta file given)	Corresponding-reads (start)	Corresponding-reads (end)	Corresponding-reads (total)
 FM_chr1_000000000001	30	chr1	260	289	chr1	56	85	GCTTACCTCTAGAATAAGTGTCAGCCAGTA	10	10	20
 FM_chr1_000000000002	30	chr1	220	249	chr1	16	45	GGATAGTGCCAAAGCTCACTCACCACTGCC	10	9	19
-FM_chr1_000000000001	30	chr1	400	429	chr1	16	45	atacgtggcatttcaggaggcggccggagg	10	10	20
+FM_chr1_000000000003	30	chr1	400	429	chr1	16	45	atacgtggcatttcaggaggcggccggagg	10	10	20
 FM_chr22_000000000001	50	chr22	100	149	chr22	16	65	AGATACAGTGTCTTTGACACGTTTATGGATTACAGCAATCACATCCAAGA	10	10	20
-FM_chr22_000000000001	30	chr22	370	399	chr22	16	45	TCTTGAGTGTTAAAATGTTGACCCCTGTAT	10	10	20
+FM_chr22_000000000002	30	chr22	370	399	chr22	16	45	TCTTGAGTGTTAAAATGTTGACCCCTGTAT	10	10	20
 FM_chrY_000000000001	30	chrY	0	29	chrY	0	29	TTGGGATGCGGGTAGTAGATGACTGCAGGG	10	9	19