| Next changeset 1:247b439a78f7 (2019-10-18) |
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Commit message:
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4 |
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gtf2gene.R gtf2gene_list.xml |
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| diff -r 000000000000 -r 040d4b3a19d5 gtf2gene.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gtf2gene.R Wed Apr 03 12:05:26 2019 -0400 |
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| @@ -0,0 +1,8 @@ +#!/usr/bin/env Rscript + +suppressPackageStartupMessages(require(rtracklayer)) +args <- commandArgs(TRUE) + +annotation <- elementMetadata(import( args[1] )) +genes <- unique(annotation[['gene_id']]) +writeLines(genes[ ! is.na(genes)], con = 'genes.txt') |
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| diff -r 000000000000 -r 040d4b3a19d5 gtf2gene_list.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gtf2gene_list.xml Wed Apr 03 12:05:26 2019 -0400 |
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| @@ -0,0 +1,54 @@ +<tool id="_ensembl_gtf2gene_list" name="GTF2GeneList" version="1.42.1+galaxy0"> + <description>extracts gene ids from Ensembl GTF using rtracklayer</description> + <requirements> + <requirement type="package" version="1.42.1">bioconductor-rtracklayer</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$gtf_input' input.gtf; + Rscript $__tool_directory__/gtf2gene.R input.gtf + ]]></command> + + <inputs> + <param name="gtf_input" type="data" format="gff" label="Ensembl GTF file" /> + </inputs> + + <outputs> + <data name="gene_list" format="tsv" from_work_dir="genes.txt" label="${tool.name} on ${on_string}"/> + </outputs> + <tests> + <test> + <param name="gtf_input" ftype="data" value="short_ensembl_gtf.gtf"/> + <output name="gene_list" ftype="data" value="genes.txt" compare="sim_size"/> + </test> + </tests> + + + <help><![CDATA[ +.. class:: infomark + +**What it does** + +Given an Ensembl GTF file, it will extract the list of all gene identifiers in the GTF to a simple tsv file. + +**Inputs** + + * Ensembl GTF file + +----- + +**Outputs** + + * Gene identifier list in tsv. +]]></help> +<citations> + <citation type="bibtex"> +@misc{github-hinxton-single-cell, +author = {Pablo Moreno, EBI Gene Expression Team}, +year = {2019}, +title = {Hinxton Single Cell Anlysis Environment}, +publisher = {GitHub}, +journal = {GitHub repository}, +url = {https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary}, + }</citation> +</citations> +</tool> |