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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
author | ebi-gxa |
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date | Wed, 03 Apr 2019 12:05:26 -0400 |
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<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>