Mercurial > repos > ebi-gxa > gtf2gene_list
comparison 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
author | ebi-gxa |
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date | Wed, 03 Apr 2019 12:05:26 -0400 |
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1 <tool id="_ensembl_gtf2gene_list" name="GTF2GeneList" version="1.42.1+galaxy0"> | |
2 <description>extracts gene ids from Ensembl GTF using rtracklayer</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.42.1">bioconductor-rtracklayer</requirement> | |
5 </requirements> | |
6 <command detect_errors="exit_code"><![CDATA[ | |
7 ln -s '$gtf_input' input.gtf; | |
8 Rscript $__tool_directory__/gtf2gene.R input.gtf | |
9 ]]></command> | |
10 | |
11 <inputs> | |
12 <param name="gtf_input" type="data" format="gff" label="Ensembl GTF file" /> | |
13 </inputs> | |
14 | |
15 <outputs> | |
16 <data name="gene_list" format="tsv" from_work_dir="genes.txt" label="${tool.name} on ${on_string}"/> | |
17 </outputs> | |
18 <tests> | |
19 <test> | |
20 <param name="gtf_input" ftype="data" value="short_ensembl_gtf.gtf"/> | |
21 <output name="gene_list" ftype="data" value="genes.txt" compare="sim_size"/> | |
22 </test> | |
23 </tests> | |
24 | |
25 | |
26 <help><![CDATA[ | |
27 .. class:: infomark | |
28 | |
29 **What it does** | |
30 | |
31 Given an Ensembl GTF file, it will extract the list of all gene identifiers in the GTF to a simple tsv file. | |
32 | |
33 **Inputs** | |
34 | |
35 * Ensembl GTF file | |
36 | |
37 ----- | |
38 | |
39 **Outputs** | |
40 | |
41 * Gene identifier list in tsv. | |
42 ]]></help> | |
43 <citations> | |
44 <citation type="bibtex"> | |
45 @misc{github-hinxton-single-cell, | |
46 author = {Pablo Moreno, EBI Gene Expression Team}, | |
47 year = {2019}, | |
48 title = {Hinxton Single Cell Anlysis Environment}, | |
49 publisher = {GitHub}, | |
50 journal = {GitHub repository}, | |
51 url = {https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary}, | |
52 }</citation> | |
53 </citations> | |
54 </tool> |