Mercurial > repos > ebi-gxa > gtf2gene_list
diff gtf2featureAnnotation.xml @ 7:14b3f2a4523b draft default tip
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml commit 5a62f18c80ddd55cfcc9d64546fde4e20be3e070"
author | ebi-gxa |
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date | Mon, 19 Jul 2021 08:00:24 +0000 |
parents | 1a642de6db01 |
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--- a/gtf2featureAnnotation.xml Wed Mar 04 06:44:32 2020 -0500 +++ b/gtf2featureAnnotation.xml Mon Jul 19 08:00:24 2021 +0000 @@ -1,13 +1,11 @@ -<tool id="_ensembl_gtf2gene_list" name="GTF2GeneList" version="1.42.1+galaxy6" profile="18.01"> +<tool id="_ensembl_gtf2gene_list" name="GTF2GeneList" version="1.52.0+galaxy0" profile="18.01"> <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> - <requirement type="package" version="2.50.2">bioconductor-biostrings</requirement> - <requirement type="package" version="1.6.4">r-optparse</requirement> + <requirement type="package" version="1.0.1">atlas-gene-annotation-manipulation</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ ln -s '$gtf_input' input.gtf; - $__tool_directory__/gtf2featureAnnotation.R --gtf-file input.gtf + gtf2featureAnnotation.R --gtf-file input.gtf #if $noheader --no-header #end if @@ -17,8 +15,17 @@ #if $mito.mark_mito --mito --mito-chr "${mito.mito_chr}" --mito-biotypes "${mito.mito_biotypes}" #end if +#if $cdnas.parse_cdnas +--parse-cdnas "${cdnas.fasta_input}" --parse-cdna-field "${cdnas.cdnas_field}" #if $cdnas.filter_cdnas ---filter-cdnas "${cdnas.fasta_input}" --filter-cdnas-field "${cdnas.cdnas_field}" --filter-cdnas-output "${fasta_output}" +--filter-cdnas-output "${fasta_output}" +#end if +#if $cdnas.parse_cdna_names +--parse-cdna-names +#end if +#if $fill_empty +--fill-empty "${fill_empty}" +#end if #end if --feature-type "${feature_type}" --first-field "${first_field}" --output-file annotation.txt --fields "${fields}" ]]></command> @@ -30,6 +37,7 @@ <param name="noheader" type="boolean" checked="false" label="Suppress header line in output?"/> <param name="fields" type="text" optional='true' value="" label="Comma-separated list of field names to extract from the GTF (default: use all fields)"/> <param name="version_transcripts" type="boolean" checked="false" label="Append version to transcript identifiers?" help="For transcript feature type only: where the GTF contains transcript versions, should these be appended to transcript identifiers? Useful when generating transcript/gene mappings for use with transcriptomes"/> + <param name="fill_empty" type="text" optional='true' value="" label="Column to be used to fill empty values in other fields" help="Only when output fields are defined, useful when you need to guarantee a value, for example a gene ID for a transcript/gene mapping."/> <conditional name="mito"> <param name="mark_mito" type="boolean" checked="true" label="Flag mitochondrial features?"/> <when value="true"> @@ -39,10 +47,12 @@ <when value="false" /> </conditional> <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)"/> + <param name="parse_cdnas" type="boolean" checked="false" label="Provide a cDNA file for extracting annotations and/ or possible filtering?" 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,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."/> + <param name="cdnas_field" type="text" optional='true' value="transcript_id" label="Annotation field in GTF to match with sequences."/> + <param name="parse_cdna_names" type="boolean" checked="false" label="Parse the FASTA headers for annotation info?" help="e.g. to find gene IDs for transcripts not present in the GTF. May only work for Ensembl GTFs."/> + <param name="filter_cdnas" type="boolean" checked="false" label="Filter the cDNA file to match the annotations?" /> </when> <when value="false" /> </conditional> @@ -67,9 +77,9 @@ **What it does** -Given an Ensembl GTF file, it will extract all information on chromosomes, coordinates, and attributes provided at the specified feature level. Mitochondrial features can also be flagged. +Given an Ensembl GTF file, it will extract all information on chromosomes, coordinates, and attributes provided at the specified feature level. Mitochondrial features can also be flagged. See https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation. -You can also supply a fasta-format file of sequences, which will be filtered by identifier to match annotation. This can be useful for tools such as Alevin which need a transcript-to-gene mapping and a transcriptome file without any missing entries (with respect to annotation). +You can also supply a fasta-format file of sequences, which can be filtered by identifier to match annotation and/or used a source of information for transcripts un-annotated in the GTF. This can be useful for tools such as Alevin which need a transcript-to-gene mapping and a transcriptome file without any missing entries (with respect to annotation). **Inputs** @@ -92,5 +102,6 @@ journal = {GitHub repository}, url = {https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary}, }</citation> + <citation type="doi">10.1101/2020.04.08.032698</citation> </citations> </tool>