Mercurial > repos > bgruening > agat

comparison macros.xml @ 2:e009d8260be2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
author bgruening
date Thu, 07 Sep 2023 05:29:24 +0000
parents 6d8444408ff1
children a6318f87f2cd
comparison
equal deleted inserted replaced
1:6d8444408ff1 2:e009d8260be2
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">1.1.0</token> 2 <token name="@TOOL_VERSION@">1.2.0</token>
3 <token name="@VERSION_SUFFIX@">1</token> 3 <token name="@VERSION_SUFFIX@">0</token>
4 <xml name="requirements"> 4 <xml name="requirements">
5 <requirements> 5 <requirements>
6 <requirement type="package" version="@TOOL_VERSION@">agat</requirement> 6 <requirement type="package" version="@TOOL_VERSION@">agat</requirement>
7 </requirements> 7 </requirements>
8 </xml> 8 </xml>
17 </citations> 17 </citations>
18 </xml> 18 </xml>
19 <xml name="ANNOTATION_INPUT" token_format="gff,gtf,gff3,gff3.gz"> 19 <xml name="ANNOTATION_INPUT" token_format="gff,gtf,gff3,gff3.gz">
20 <param argument="--gff" type="data" format="@FORMAT@" label="Annotation file" help="Input GTF/GFF file" /> 20 <param argument="--gff" type="data" format="@FORMAT@" label="Annotation file" help="Input GTF/GFF file" />
21 </xml> 21 </xml>
22 22 <xml name="AGAT_CONFIG">
23 <conditional name="output_format">
24 <param name="selector" type="select" label="Output format">
25 <option value="GFF">GFF</option>
26 <option value="GTF">GTF</option>
27 </param>
28 <when value="GFF">
29 <param name="version" type="select" label="Format version">
30 <option value="1">1</option>
31 <option value="2">2</option>
32 <option value="2.5">2.5</option>
33 <option value="3" selected="true">3</option>
34 </param>
35 </when>
36 <when value="GTF">
37 <param name="version" type="select" label="Format version">
38 <option value="1">1 = ("CDS", "start_codon", "stop_codon", "exon", "intron")</option>
39 <option value="2">2 = ("CDS", "start_codon", "stop_codon", "exon")</option>
40 <option value="2.1">2.1 = ("CDS", "start_codon", "stop_codon", "exon", "5UTR", "3UTR")</option>
41 <option value="2.2">2.2 = ("CDS", "start_codon", "stop_codon", "5UTR", "3UTR", "inter", "inter_CNS", "intron_CNS", "exon")</option>
42 <option value="2.5">2.5 = ("gene", "transcript", "exon", "CDS", "UTR", "start_codon", "stop_codon", "Selenocysteine")</option>
43 <option value="3">3 = ("gene", "transcript", "exon", "CDS", "Selenocysteine", "start_codon", "stop_codon", "three_prime_utr", "five_prime_utr")</option>
44 <option value="relax" selected="true">Relax = All feature types will be accepted</option>
45 </param>
46 </when>
47 </conditional>
48 <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." />
49 <param name="create_exon" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Create exon when l2 do not have children"/>
50 </xml>
51
23 <xml name="REFERENCE_FASTA"> 52 <xml name="REFERENCE_FASTA">
24 <conditional name="reference_genome"> 53 <conditional name="reference_genome">
25 <param name="source" type="select" label="Source for the reference genome" help="Built-in references were created using default options."> 54 <param name="source" type="select" label="Source for the reference genome" help="Built-in references were created using default options.">
26 <option value="indexed" selected="true">Use a built-in genome</option> 55 <option value="indexed" selected="true">Use a built-in genome</option>
27 <option value="history" selected="true">Use a genome from history</option> 56 <option value="history" selected="true">Use a genome from history</option>