Repository revision
7:14b3f2a4523b

Repository 'gtf2gene_list'
hg clone https://toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list

GTF2GeneList tool metadata
Miscellaneous
GTF2GeneList
extracts a complete annotation table or subsets thereof from an Ensembl GTF using rtracklayer
_ensembl_gtf2gene_list
toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.52.0+galaxy0
1.52.0+galaxy0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.52.0+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.42.1+galaxy6
toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.42.1+galaxy5
toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.42.1+galaxy4
toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.42.1+galaxy3
toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.42.1+galaxy2
toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.42.1+galaxy1
toolshed.g2.bx.psu.edu/repos/ebi-gxa/gtf2gene_list/_ensembl_gtf2gene_list/1.42.1+galaxy0
_ensembl_gtf2gene_list
Requirements (dependencies defined in the <requirements> tag set)
name version type
atlas-gene-annotation-manipulation 1.0.1 package
Additional information about this tool
ln -s '$gtf_input' input.gtf;
       gtf2featureAnnotation.R --gtf-file input.gtf
#if $noheader
--no-header
#end if
#if $version_transcripts
--version-transcripts
#end if
#if $mito.mark_mito
--mito --mito-chr "${mito.mito_chr}" --mito-biotypes "${mito.mito_biotypes}"
#end if
#if $cdnas.parse_cdnas
--parse-cdnas "${cdnas.fasta_input}" --parse-cdna-field "${cdnas.cdnas_field}" 
#if $cdnas.filter_cdnas
--filter-cdnas-output "${fasta_output}"
#end if
#if $cdnas.parse_cdna_names
--parse-cdna-names
#end if
#if $fill_empty
--fill-empty "${fill_empty}"
#end if
#end if
--feature-type "${feature_type}" --first-field "${first_field}" --output-file annotation.txt --fields "${fields}"
	    
None
False
Functional tests
name inputs outputs required files
Test-1 gtf_input: test.gtf
name: value
test.gtf
value