Mercurial > repos > ebi-gxa > gtf2gene_list

comparison gtf2featureAnnotation.xml @ 6:1a642de6db01 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml commit bf9021c853da640771202920cde38f77cdeaf368"
author ebi-gxa
date Wed, 04 Mar 2020 06:44:32 -0500
parents 00ee933b08fd
children 14b3f2a4523b
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5:00ee933b08fd 6:1a642de6db01
1 <tool id="_ensembl_gtf2gene_list" name="GTF2GeneList" version="1.42.1+galaxy5"> 1 <tool id="_ensembl_gtf2gene_list" name="GTF2GeneList" version="1.42.1+galaxy6" profile="18.01">
2 <description>extracts a complete annotation table or subsets thereof from an Ensembl GTF using rtracklayer</description> 2 <description>extracts a complete annotation table or subsets thereof from an Ensembl GTF using rtracklayer</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.42.1">bioconductor-rtracklayer</requirement> 4 <requirement type="package" version="1.42.1">bioconductor-rtracklayer</requirement>
5 <requirement type="package">bioconductor-biostrings</requirement> 5 <requirement type="package" version="2.50.2">bioconductor-biostrings</requirement>
6 <requirement type="package">r-optparse</requirement> 6 <requirement type="package" version="1.6.4">r-optparse</requirement>
7 </requirements> 7 </requirements>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 ln -s '$gtf_input' input.gtf; 9 ln -s '$gtf_input' input.gtf;
10 $__tool_directory__/gtf2featureAnnotation.R --gtf-file input.gtf 10 $__tool_directory__/gtf2featureAnnotation.R --gtf-file input.gtf
11 #if $noheader 11 #if $noheader
13 #end if 13 #end if
14 #if $version_transcripts 14 #if $version_transcripts
15 --version-transcripts 15 --version-transcripts
16 #end if 16 #end if
17 #if $mito.mark_mito 17 #if $mito.mark_mito
18 --mito --mito-chr "${mito.mito_chr}" --mito-biotypes "${mito.mito_biotypes}" 18 --mito --mito-chr "${mito.mito_chr}" --mito-biotypes "${mito.mito_biotypes}"
19 #end if 19 #end if
20 #if $cdnas.filter_cdnas 20 #if $cdnas.filter_cdnas
21 --filter-cdnas "${cdnas.fasta_input}" --filter-cdnas-field "${cdnas.cdnas_field}" --filter-cdnas-output "${fasta_output}" 21 --filter-cdnas "${cdnas.fasta_input}" --filter-cdnas-field "${cdnas.cdnas_field}" --filter-cdnas-output "${fasta_output}"
22 #end if 22 #end if
23 --feature-type "${feature_type}" --first-field "${first_field}" --output-file annotation.txt --fields "${fields}" 23 --feature-type "${feature_type}" --first-field "${first_field}" --output-file annotation.txt --fields "${fields}"