| Previous changeset 2:e255c0e5dfca (2019-10-18) Next changeset 4:b6354c917ef9 (2019-10-25) |
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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 194d2e0af16624c9a3d1af92f7b3686d2e0ee552-dirty |
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modified:
gtf2featureAnnotation.xml |
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| diff -r e255c0e5dfca -r b95e6a9bb15c gtf2featureAnnotation.xml --- a/gtf2featureAnnotation.xml Fri Oct 18 11:00:04 2019 -0400 +++ b/gtf2featureAnnotation.xml Tue Oct 22 05:49:12 2019 -0400 |
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| @@ -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> |