Mercurial > repos > yhoogstrate > flaimapper
changeset 7:0ea90514e0a0 draft
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit beb30713f9b8510c22f46d94cb58c92cf26c799c
| author | erasmus-medical-center |
|---|---|
| date | Fri, 28 Apr 2017 07:05:48 -0400 |
| parents | c143e7e1fdbf |
| children | 4f22bd612754 |
| files | flaimapper.xml test-data/snord81.flaimapper.duck-15.gtf test-data/snord81.flaimapper.gtf test-data/snord81.flaimapper.offsets_5_5.gtf test-data/test_genomic_flaimapper_output.gtf |
| diffstat | 5 files changed, 36 insertions(+), 35 deletions(-) [+] |
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--- 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>&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>
--- 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"
--- 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"
--- 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"
--- 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"