Mercurial > repos > bgruening > agat
view macros.xml @ 3:a6318f87f2cd draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
author | bgruening |
---|---|
date | Thu, 15 Feb 2024 15:47:19 +0000 |
parents | e009d8260be2 |
children | abba05ead5d7 |
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<macros> <token name="@TOOL_VERSION@">1.2.0</token> <token name="@VERSION_SUFFIX@">1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">agat</requirement> </requirements> </xml> <xml name="biotools"> <xrefs> <xref type="bio.tools">agat</xref> </xrefs> </xml> <xml name="citations"> <citations> <citation type="doi">10.5281/zenodo.3552717</citation> </citations> </xml> <xml name="ANNOTATION_INPUT" token_format="gff,gtf,gff3,gff3.gz"> <param argument="--gff" type="data" format="@FORMAT@" label="Annotation file" help="Input GTF/GFF file" /> </xml> <xml name="AGAT_CONFIG"> <conditional name="output_format"> <param name="selector" type="select" label="Output format"> <option value="GFF">GFF</option> <option value="GTF">GTF</option> </param> <when value="GFF"> <param name="version" type="select" label="Format version"> <option value="1">1</option> <option value="2">2</option> <option value="2.5">2.5</option> <option value="3" selected="true">3</option> </param> </when> <when value="GTF"> <param name="version" type="select" label="Format version"> <option value="1">1 = ("CDS", "start_codon", "stop_codon", "exon", "intron")</option> <option value="2">2 = ("CDS", "start_codon", "stop_codon", "exon")</option> <option value="2.1">2.1 = ("CDS", "start_codon", "stop_codon", "exon", "5UTR", "3UTR")</option> <option value="2.2">2.2 = ("CDS", "start_codon", "stop_codon", "5UTR", "3UTR", "inter", "inter_CNS", "intron_CNS", "exon")</option> <option value="2.5">2.5 = ("gene", "transcript", "exon", "CDS", "UTR", "start_codon", "stop_codon", "Selenocysteine")</option> <option value="3">3 = ("gene", "transcript", "exon", "CDS", "Selenocysteine", "start_codon", "stop_codon", "three_prime_utr", "five_prime_utr")</option> <option value="relax" selected="true">Relax = All feature types will be accepted</option> </param> </when> </conditional> <param name="merge_loci" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Merge loci" help="Should overlapping loci (at CDS level) be merged in a single locus. Only one gene is kept, and the mRNA features become isoforms." /> <param name="create_exon" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Create exon when l2 do not have children"/> </xml> <xml name="REFERENCE_FASTA"> <conditional name="reference_genome"> <param name="source" type="select" label="Source for the reference genome" help="Built-in references were created using default options."> <option value="indexed" selected="true">Use a built-in genome</option> <option value="history" selected="true">Use a genome from history</option> </param> <when value="indexed"> <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team."> <options from_data_table="fasta_indexes"> <filter type="sort_by" column="2" /> <validator type="no_options" message="No genomes are available for the selected input dataset" /> </options> </param> </when> <when value="history"> <param name="history_item" type="data" format="fasta" label="Reference genome" help="A reference genome in FASTA format" /> </when> </conditional> </xml> <token name="@input_annotation_single@"><![CDATA[ #set $input_annotation = 'annotation.' + str($tool.gff.ext) ln -s '${tool.gff}' $input_annotation && ]]></token> <token name="@input_reference@"><![CDATA[ #if $tool.reference_genome.source == 'history': #set $ref_genome = 'reference.fasta' ln -s -f '${tool.reference_genome.history_item}' '$ref_genome' && #else: #set $ref_genome = $tool.reference_genome.index.fields.path #end if ]]></token> <token name="@input_annotation_double@"><![CDATA[ #set $input1 = 'annotation1.' + str($tool.input_annotation1.ext) #set $input2 = 'annotation2.' + str($tool.input_annotation2.ext) ln -s '${tool.input_annotation1}' '$input1' && ln -s '${tool.input_annotation2}' '$input2' && ]]></token> </macros>