annotate gtf2gene_list.xml @ 0:040d4b3a19d5 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4

<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>