Mercurial > repos > ebi-gxa > gtf2gene_list
changeset 3:b95e6a9bb15c draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552-dirty
| author | ebi-gxa |
|---|---|
| date | Tue, 22 Oct 2019 05:49:12 -0400 |
| parents | e255c0e5dfca |
| children | b6354c917ef9 |
| files | gtf2featureAnnotation.xml |
| diffstat | 1 files changed, 3 insertions(+), 3 deletions(-) [+] |
line wrap: on
line diff
--- a/gtf2featureAnnotation.xml Fri Oct 18 11:00:04 2019 -0400 +++ b/gtf2featureAnnotation.xml Tue Oct 22 05:49:12 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="_ensembl_gtf2gene_list" name="GTF2GeneList" version="1.42.1+galaxy2"> +<tool id="_ensembl_gtf2gene_list" name="GTF2GeneList" version="1.42.1+galaxy3"> <description>extracts a complete annotation table or subsets thereof from an Ensembl GTF using rtracklayer</description> <requirements> <requirement type="package" version="1.42.1">bioconductor-rtracklayer</requirement> @@ -41,7 +41,7 @@ <conditional name="cdnas"> <param name="filter_cdnas" type="boolean" checked="false" label="Filter a FASTA-format cDNA file to match annotations?" help="For some applications, e.g. transcriptome mappers, its useful to match a cDNAs file to an annotation list (e.g. transcript-to-gene mapping)"/> <when value="true"> - <param name="fasta_input" type="data" format="fasta" label="FASTA-format cDNA/ transcript file" /> + <param name="fasta_input" type="data" format="fasta,fasta.gz" label="FASTA-format cDNA/ transcript file" /> <param name="cdnas_field" type="text" optional='true' value="transcript_id" label="Annotation field to match with sequences."/> </when> <when value="false" /> @@ -50,7 +50,7 @@ <outputs> <data name="feature_annotation" format="tsv" from_work_dir="annotation.txt" label="${tool.name} on ${on_string}: annotation table"/> - <data name="fasta_output" format="fasta" from_work_dir="filtered.fa.gz" label="${tool.name} on ${on_string}: annotation-matched sequences"> + <data name="fasta_output" format="fasta.gz" from_work_dir="filtered.fa.gz" label="${tool.name} on ${on_string}: annotation-matched sequences"> <filter>filter_cdnas</filter> </data> </outputs>