Mercurial > repos > gga > chado_feature_load_gff

comparison feature_load_gff.xml @ 4:3a36c33f7a49 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit d21999bb3e142fd972a3338b70216989a257d5b1
author gga
date Mon, 06 Aug 2018 04:42:17 -0400
parents 04f12e56d4c7
children c510dc82df88
comparison
equal deleted inserted replaced
3:bbd39fc418cc 4:3a36c33f7a49
49 dynamic_options="list_organisms()" 49 dynamic_options="list_organisms()"
50 label="Organism" /> 50 label="Organism" />
51 51
52 <!-- options --> 52 <!-- options -->
53 <param name="landmark_type" label="Landmark Type" argument="landmark_type" type="text" help="Type of the landmarks (will speed up loading if provided, e.g. contig, should be a term of the Sequence ontology)" /> 53 <param name="landmark_type" label="Landmark Type" argument="landmark_type" type="text" help="Type of the landmarks (will speed up loading if provided, e.g. contig, should be a term of the Sequence ontology)" />
54 <param name="re_protein_capture" label="Regex protein capture" argument="re_protein_capture" type="text" help="Regular expression to capture groups in mRNA name to use in 'Regex protein' (e.g. '^(.*?)-R([A-Z]+)$', default='^(.*?)$' )" /> 54 <param name="re_protein_capture" label="Regex protein capture" argument="re_protein_capture" type="text" help="Regular expression to capture groups in mRNA name to use in 'Regex protein' (e.g. '^(.*?)-R([A-Z]+)$', default='^(.*?)$' )">
55 <param name="re_protein" label="Regex protein" argument="re_protein" type="text" help="Replacement string for the protein name using capturing groups defined in 'Regex protein capture'" /> 55 <expand macro="sanitized"/>
56 </param>
57 <param name="re_protein" label="Regex protein" argument="re_protein" type="text" help="Replacement string for the protein name using capturing groups defined in 'Regex protein capture' (e.g. '\1-P\2')">
58 <expand macro="sanitized"/>
59 </param>
56 <param name="fasta" label="Fasta" argument="fasta" type="data" format="fasta" help="A Fasta containing sequences for some features. When creating a feature, if its sequence is in this fasta file it will be loaded. Otherwise for mRNA and polypeptides it will be computed from the genome sequence (if available), otherwise it will be left empty." optional="true" /> 60 <param name="fasta" label="Fasta" argument="fasta" type="data" format="fasta" help="A Fasta containing sequences for some features. When creating a feature, if its sequence is in this fasta file it will be loaded. Otherwise for mRNA and polypeptides it will be computed from the genome sequence (if available), otherwise it will be left empty." optional="true" />
57 <param name="no_seq_compute" label="Allow computing missing sequences" argument="no_seq_compute" type="boolean" truevalue="" falsevalue="--no_seq_compute" help="Enable the computation of mRNA and polypeptides sequences based on genome sequence and positions." /> 61 <param name="no_seq_compute" label="Allow computing missing sequences" argument="no_seq_compute" type="boolean" truevalue="" falsevalue="--no_seq_compute" help="Enable the computation of mRNA and polypeptides sequences based on genome sequence and positions." />
58 <param name="add_only" label="Add only" argument="add_only" type="boolean" truevalue="--add_only" falsevalue="" help="Use this flag if you're not updating existing features, but just adding new features to the selected analysis and organism. It will speedup loading, and reduce memory usage, but might produce errors in case of already existing feature." /> 62 <param name="add_only" label="Add only" argument="add_only" type="boolean" truevalue="--add_only" falsevalue="" help="Use this flag if you're not updating existing features, but just adding new features to the selected analysis and organism. It will speedup loading, and reduce memory usage, but might produce errors in case of already existing feature." />
59 63
60 <expand macro="wait_for"/> 64 <expand macro="wait_for"/>