ncbi_datasets: datasets_gene.xml annotate

annotate datasets_gene.xml @ 20:35d32c807c23 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb

author	iuc
date	Fri, 26 Dec 2025 17:16:51 +0000
parents	9a10a6449901
children

rev	line source
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	1 <tool id="datasets_download_gene" name="NCBI Datasets Gene" profile="@PROFILE@" license="@LICENSE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	2 <description>download gene sequences and metadata</description>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	3 <macros>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	4 <import>macros.xml</import>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	5 </macros>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	6 <expand macro="bio_tools"/>
20 35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	7 <expand macro="requirements"/>
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	8 <expand macro="version_command"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	9 <command><![CDATA[
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	10 #import re
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	11 @SETUP_CERTIFICATES@
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	12 datasets download gene $query.subcommand.download_by
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	13 #if $query.subcommand.download_by == 'taxon':
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	14 '$query.subcommand.taxon_positional'
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	15 #else:
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	16 #if $query.subcommand.text_or_file.text_or_file == 'text':
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	17 #echo " ".join(f"'{x}'" for x in re.split(" \|,", str($query.subcommand.text_or_file.accession)) if x)
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	18 #else
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	19 --inputfile '$query.subcommand.text_or_file.inputfile'
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	20 #end if
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	21 #end if
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	22
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	23 #if $query.subcommand.download_by != 'taxon' and $query.subcommand.ortholog:
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	24 --ortholog '$query.subcommand.ortholog'
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	25 #end if
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	26
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	27 #if $query.subcommand.download_by == 'symbol':
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	28 #if $query.subcommand.taxon
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	29 --taxon '$query.subcommand.taxon'
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	30 #end if
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	31 #end if
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	32
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	33 #if $query.subcommand.download_by == 'accession':
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	34 #if $query.subcommand.taxon_filter
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	35 --taxon-filter '$query.subcommand.taxon_filter'
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	36 #end if
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	37 #if str($query.subcommand.include_flanks_bp)
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	38 --include-flanks-bp $query.subcommand.include_flanks_bp
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	39 #end if
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	40 #end if
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	41
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	42 #if $filters.fasta_filter_cond.fasta_filter_select
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	43 #if $filters.fasta_filter_cond.fasta_filter_select == 'text'
20 35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	44 --fasta-filter #echo ",".join(f"'{x}'" for x in str($filters.fasta_filter_cond.fasta_filter).split(',') if x)
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	45 #else
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	46 --fasta-filter-file '$filters.fasta_filter_cond.fasta_filter_file'
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	47 #end if
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	48 #end if
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	49
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	50 --include
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	51 #if $file_choices.kingdom_cond.include
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	52 #echo ",".join($file_choices.kingdom_cond.include)
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	53 #else
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	54 none
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	55 #end if
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	56
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	57 --no-progressbar
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	58
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	59 ## produce TSV report file (either gene or prok-gene)
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	60 &&
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	61 dataformat
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	62 tsv
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	63 $file_choices.kingdom_cond.kingdom_sel
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	64 --package ncbi_dataset.zip
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	65 --fields #echo ",".join($file_choices.kingdom_cond.report_columns)
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	66 > gene_data_report.tsv
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	67 ## if ! dataformat tsv gene --package ncbi_dataset.zip > gene_data_report.tsv 2> dataformat.log; then
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	68 ## dataformat tsv prok-gene --package ncbi_dataset.zip > gene_data_report.tsv 2>> dataformat.log;
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	69 ## fi
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	70
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	71 #if $file_choices.kingdom_cond.include and "product-report" in $file_choices.kingdom_cond.include
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	72 && dataformat tsv gene-product --package ncbi_dataset.zip > gene_product_report.tsv
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	73 #end if
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	74
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	75 ## unzip and rehydrate if any data is to be downloaded (include is not None)
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	76 #if $file_choices.kingdom_cond.include
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	77 ## unzip
16 9a10a6449901 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b iuc parents: 15 diff changeset	78 && unzip ncbi_dataset.zip
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	79 #end if
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	80 ]]></command>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	81 <inputs>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	82 <section name="query" title="Query" expanded="true">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	83 <conditional name="subcommand">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	84 <param name="download_by" type="select" label="Choose how to find genes to download">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	85 <option value="gene-id">By NCBI Gene ID</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	86 <option value="symbol">By Gene symbol</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	87 <option value="accession">By RefSeq nucleotide or protein accession</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	88 <option value="taxon">By taxon (NCBI Taxonomy ID, scientific or common name at any tax rank)</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	89 </param>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	90 <when value="gene-id">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	91 <expand macro="text_or_file" what="Gene ID" what_extended="NCBI Gene ID" help=""/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	92 <expand macro="ortholog"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	93 </when>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	94 <when value="symbol">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	95 <expand macro="text_or_file" what="Gene Symbol" what_extended="NCBI Gene Symbol" help=""/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	96 <expand macro="ortholog"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	97 <param argument="--taxon" type="text" value="human" label="Species for gene symbol" help="NCBI taxid, common or scientific name">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	98 <sanitizer invalid_char="">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	99 <valid initial="string.letters">
20 35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	100 <add value=" "/>
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	101 <add value="-"/>
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	102 </valid>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	103 </sanitizer>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	104 </param>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	105 </when>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	106 <when value="accession">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	107 <expand macro="text_or_file" what="Gene Accession" what_extended="NCBI Gene Accession" help=""/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	108 <expand macro="ortholog"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	109 <param argument="--taxon-filter" type="text" value="" label="Limit gene sequences and annotation report file to specified taxon" help="any rank, only available for WP accessions">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	110 <sanitizer invalid_char="">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	111 <valid initial="string.letters">
20 35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	112 <add value=" "/>
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	113 <add value="-"/>
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	114 </valid>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	115 </sanitizer>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	116 </param>
16 9a10a6449901 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b iuc parents: 15 diff changeset	117 <param argument="--include-flanks-bp" type="integer" optional="true" min="0" value="" label="Length of flanking nucleotides" help="WP accessions only"/>
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	118 </when>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	119 <when value="taxon">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	120 <expand macro="taxon_positional"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	121 </when>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	122 </conditional>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	123 </section>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	124 <section name="filters" title="Filters and Limit">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	125 <conditional name="fasta_filter_cond" label="Filter protein and RNA sequences by RefSeq nucleotide and protein accessions">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	126 <param name="fasta_filter_select" type="select" label="Apply filter">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	127 <option value="">No</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	128 <option value="text">Enter accessions</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	129 <option value="file">Read a list of accessions from a dataset</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	130 </param>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	131 <when value=""/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	132 <when value="text">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	133 <param argument="--fasta-filter" type="text" label="RefSeq nucleotide and protein accessions" help="Comma separated">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	134 <sanitizer invalid_char="">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	135 <valid initial="string.letters,string.digits">
20 35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	136 <add value=","/>
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	137 </valid>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	138 </sanitizer>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	139 </param>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	140 </when>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	141 <when value="file">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	142 <param argument="--fasta-filter-file" type="data" format="txt" label="Dataset with list of RefSeq nucleotide and protein accessions" help=""/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	143 </when>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	144 </conditional>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	145 </section>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	146 <section name="file_choices" title="Output options" expanded="true">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	147 <conditional name="kingdom_cond">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	148 <param name="kingdom_sel" type="select" label="Kingdom" help="Prokaryotic: Accessions starting with WP_. Data report has a different format and the rna, cds, 3/5' UTR and gene-product report are not suported. ">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	149 <option value="gene">Eukaryote</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	150 <option value="prok-gene">Prokaryote</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	151 </param>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	152 <when value="gene">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	153 <expand macro="gene_tsv_report_columns">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	154 <option value="gene-id" selected="true">NCBI GeneID</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	155 <option value="gene-type" selected="true">Gene Type</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	156 <option value="common-name" selected="true">Common Name</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	157 <option value="description" selected="true">Description</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	158 <option value="symbol" selected="true">Symbol</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	159 <option value="synonyms" selected="true">Synonyms</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	160 <option value="tax-id" selected="true">Taxonomic ID</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	161 <option value="tax-name" selected="true">Taxonomic Name</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	162 </expand>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	163 <expand macro="include">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	164 <expand macro="gene_includes">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	165 <option value="rna" selected="true">transcript (rna)</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	166 <option value="cds">nucleotide coding sequences (cds)</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	167 <option value="5p-utr">5'-UTR (5p-utr)</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	168 <option value="3p-utr">3'-UTR (3p-utr)</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	169 <option value="product-report"> (product-report)</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	170 </expand>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	171 </expand>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	172 </when>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	173 <when value="prok-gene">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	174 <expand macro="prok_gene_tsv_report_columns">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	175 <option value="accession" selected="true">Accession</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	176 <option value="description" selected="true">Description</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	177 <option value="ec-number" selected="true">EC Number</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	178 <option value="gene-symbol" selected="true">Gene Symbol</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	179 <option value="mapping-count" selected="true">Number of Genome Mappings</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	180 <option value="protein-length" selected="true">Protein Length</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	181 <option value="protein-name" selected="true">Protein Name</option>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	182 </expand>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	183 <expand macro="include">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	184 <expand macro="gene_includes"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	185 </expand>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	186 </when>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	187 </conditional>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	188 <param name="decompress" type="boolean" label="Decompress FASTA" help="By default FASTA files are provided zipped (fasta.gz) if this is checked the data will be decompressed"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	189 </section>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	190 </inputs>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	191 <outputs>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	192 <data name="gene_data_report" format="tabular" label="NCBI Gene Datasets: Data Report" from_work_dir="gene_data_report.tsv"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	193 <data name="gene_product_report" format="tabular" label="NCBI Gene Datasets: Product Report" from_work_dir="gene_product_report.tsv">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	194 <filter>file_choices['kingdom_cond']['include'] and "product-report" in file_choices['kingdom_cond']['include']</filter>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	195 </data>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	196 <data name="gene_fasta" label="NCBI Gene Datasets: Gene fasta" format="fasta" from_work_dir="ncbi_dataset/data/gene.fna">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	197 <filter>file_choices['kingdom_cond']['include'] and "gene" in file_choices['kingdom_cond']['include']</filter>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	198 </data>
16 9a10a6449901 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b iuc parents: 15 diff changeset	199 <data name="gene_flanks" label="NCBI Gene Datasets: Flanking faste" format="fasta" from_work_dir="ncbi_dataset/data/gene_flank.fna">
9a10a6449901 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b iuc parents: 15 diff changeset	200 <filter>query['subcommand']['download_by'] == "accession" and query['subcommand']['include_flanks_bp'] != ""</filter>
9a10a6449901 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b iuc parents: 15 diff changeset	201 </data>
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	202 <data name="rna_fasta" label="NCBI Gene Datasets: RNA fasta" format="fasta" from_work_dir="ncbi_dataset/data/rna.fna">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	203 <filter>file_choices['kingdom_cond']['include'] and "rna" in file_choices['kingdom_cond']['include']</filter>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	204 </data>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	205 <data name="protein_fasta" label="NCBI Gene Datasets: protein fasta" format="fasta" from_work_dir="ncbi_dataset/data/protein.faa">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	206 <filter>file_choices['kingdom_cond']['include'] and "protein" in file_choices['kingdom_cond']['include']</filter>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	207 </data>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	208 <data name="cds_fasta" label="NCBI Gene Datasets: CDS fasta" format="fasta" from_work_dir="ncbi_dataset/data/cds.fna">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	209 <filter>file_choices['kingdom_cond']['include'] and "cds" in file_choices['kingdom_cond']['include']</filter>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	210 </data>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	211 <data name="threep_utr_fasta" label="NCBI Gene Datasets: 3' UTR fasta" format="fasta" from_work_dir="ncbi_dataset/data/3p_utr.fna">
20 35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	212 <filter>file_choices['kingdom_cond']['include'] and "3p-utr" in file_choices['kingdom_cond']['include']</filter>
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	213 </data>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	214 <data name="fivep_utr_fasta" label="NCBI Gene Datasets: 5' UTR fasta" format="fasta" from_work_dir="ncbi_dataset/data/5p_utr.fna">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	215 <filter>file_choices['kingdom_cond']['include'] and "5p-utr" in file_choices['kingdom_cond']['include']</filter>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	216 </data>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	217 </outputs>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	218 <tests>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	219 <!-- 1: datasets download gene gene-id 672 -->
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	220 <test expect_num_outputs="3">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	221 <conditional name="query\|subcommand">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	222 <param name="download_by" value="gene-id"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	223 <conditional name="text_or_file">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	224 <param name="text_or_file" value="text"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	225 <param name="accession" value="672"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	226 </conditional>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	227 </conditional>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	228 <output name="gene_data_report">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	229 <assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	230 <has_text text="human"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	231 <has_text text="BRCA1"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	232 <has_n_lines n="2"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	233 <has_n_columns n="8"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	234 </assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	235 </output>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	236 <output name="rna_fasta">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	237 <assert_contents>
20 35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	238 <has_text text=">"/>
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	239 </assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	240 </output>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	241 <output name="protein_fasta">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	242 <assert_contents>
20 35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	243 <has_text text=">"/>
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	244 </assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	245 </output>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	246 </test>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	247 <!-- 2: datasets download gene gene-id 2597 14433 -->
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	248 <test expect_num_outputs="3">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	249 <conditional name="query\|subcommand">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	250 <param name="download_by" value="gene-id"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	251 <conditional name="text_or_file">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	252 <param name="text_or_file" value="text"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	253 <param name="accession" value="2597,14433"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	254 </conditional>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	255 </conditional>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	256 <output name="gene_data_report">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	257 <assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	258 <has_text text="house mouse"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	259 <has_text text="glyceraldehyde-3-phosphate dehydrogenase"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	260 <has_n_lines n="3"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	261 <has_n_columns n="8"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	262 </assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	263 </output>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	264 <output name="rna_fasta">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	265 <assert_contents>
20 35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	266 <has_text text=">"/>
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	267 </assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	268 </output>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	269 <output name="protein_fasta">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	270 <assert_contents>
20 35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	271 <has_text text=">"/>
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	272 </assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	273 </output>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	274 </test>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	275 <!-- 3: same as above + give accessions by file, 2 different outputs and ortholog-->
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	276 <test expect_num_outputs="3">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	277 <conditional name="query\|subcommand">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	278 <param name="download_by" value="gene-id"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	279 <conditional name="text_or_file">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	280 <param name="text_or_file" value="file"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	281 <param name="inputfile" value="geneids.txt"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	282 </conditional>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	283 <param name="ortholog" value="Haplorrhini,Strepsirrhini"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	284 </conditional>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	285 <section name="file_choices">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	286 <conditional name="kingdom_cond">
20 35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	287 <param name="kingdom_sel" value="gene"/>
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	288 <param name="include" value="gene,cds"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	289 </conditional>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	290 </section>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	291 <output name="gene_data_report">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	292 <assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	293 <has_text text="baboon"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	294 <has_text text="glyceraldehyde-3-phosphate dehydrogenase"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	295 <has_n_lines min="30"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	296 <has_n_columns n="8"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	297 </assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	298 </output>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	299 <output name="gene_fasta">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	300 <assert_contents>
20 35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	301 <has_text text=">"/>
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	302 </assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	303 </output>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	304 <output name="cds_fasta">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	305 <assert_contents>
20 35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	306 <has_text text=">"/>
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	307 </assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	308 </output>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	309 </test>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	310 <!-- 4: datasets download gene symbol tp53 -->
20 35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	311 <test expect_num_outputs="3">
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	312 <conditional name="query\|subcommand">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	313 <param name="download_by" value="symbol"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	314 <conditional name="text_or_file">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	315 <param name="text_or_file" value="text"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	316 <param name="accession" value="tp53"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	317 </conditional>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	318 </conditional>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	319 <output name="gene_data_report">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	320 <assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	321 <has_text text="human"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	322 <has_n_lines n="2"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	323 <has_n_columns n="8"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	324 </assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	325 </output>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	326 </test>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	327 <!-- 5: datasets download gene symbol brca1 \-\-taxon mouse -->
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	328 <test expect_num_outputs="4">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	329 <conditional name="query\|subcommand">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	330 <param name="download_by" value="symbol"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	331 <conditional name="text_or_file">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	332 <param name="text_or_file" value="text"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	333 <param name="accession" value="brca1"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	334 </conditional>
16 9a10a6449901 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b iuc parents: 15 diff changeset	335 <param name="taxon" value="house mouse"/>
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	336 </conditional>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	337 <section name="file_choices">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	338 <conditional name="kingdom_cond">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	339 <param name="include" value="3p-utr,5p-utr,product-report"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	340 </conditional>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	341 </section>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	342 <output name="gene_data_report">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	343 <assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	344 <has_text text="house mouse"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	345 <has_text text="Brca1"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	346 <has_n_lines n="2"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	347 <has_n_columns n="8"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	348 </assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	349 </output>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	350 <output name="gene_product_report">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	351 <assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	352 <has_text text="house mouse"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	353 <has_text text="XR_004936704.1"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	354 <has_n_lines min="130"/>
16 9a10a6449901 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b iuc parents: 15 diff changeset	355 <has_n_columns n="39"/>
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	356 </assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	357 </output>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	358 <output name="threep_utr_fasta">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	359 <assert_contents>
20 35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	360 <has_text text=">"/>
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	361 </assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	362 </output>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	363 <output name="fivep_utr_fasta">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	364 <assert_contents>
20 35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	365 <has_text text=">"/>
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	366 </assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	367 </output>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	368 </test>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	369 <!-- 6: datasets download gene symbol brca1 \-\-ortholog -->
20 35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	370 <test expect_num_outputs="3">
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	371 <conditional name="query\|subcommand">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	372 <param name="download_by" value="symbol"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	373 <conditional name="text_or_file">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	374 <param name="text_or_file" value="text"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	375 <param name="accession" value="brca1"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	376 </conditional>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	377 <param name="ortholog" value="rodentia"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	378 </conditional>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	379 <output name="gene_data_report">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	380 <assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	381 <has_text text="rat"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	382 <has_text text="Brca1"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	383 <has_n_lines min="30"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	384 <has_n_columns n="8"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	385 </assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	386 </output>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	387 </test>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	388 <!-- 7: datasets download gene accession NP_000483.3 -->
20 35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	389 <test expect_num_outputs="3">
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	390 <conditional name="query\|subcommand">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	391 <param name="download_by" value="accession"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	392 <conditional name="text_or_file">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	393 <param name="text_or_file" value="text"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	394 <param name="accession" value="NP_000483.3"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	395 </conditional>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	396 </conditional>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	397 <output name="gene_data_report">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	398 <assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	399 <has_text text="human"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	400 <has_n_lines n="2"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	401 <has_n_columns n="8"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	402 </assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	403 </output>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	404 </test>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	405 <!-- 8: datasets download gene accession NM_000546.6 NM_000492.4 + ortholog-->
20 35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	406 <test expect_num_outputs="3">
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	407 <conditional name="query\|subcommand">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	408 <param name="download_by" value="accession"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	409 <conditional name="text_or_file">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	410 <param name="text_or_file" value="text"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	411 <param name="accession" value="NM_000546.6 NM_000492.4"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	412 </conditional>
15 dfad868c911b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 390b8177036c256e7e870dfe67c6de7d6417ad39 iuc parents: 14 diff changeset	413 <param name="ortholog" value="all"/>
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	414 </conditional>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	415 <output name="gene_data_report">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	416 <assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	417 <has_text text="human"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	418 <has_n_lines min="800"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	419 <has_n_columns n="8"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	420 </assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	421 </output>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	422 </test>
16 9a10a6449901 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b iuc parents: 15 diff changeset	423 <!-- 9: datasets download gene accession WP_003249567.1 + include_flanks_bp -->
9a10a6449901 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b iuc parents: 15 diff changeset	424 <test expect_num_outputs="4">
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	425 <conditional name="query\|subcommand">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	426 <param name="download_by" value="accession"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	427 <conditional name="text_or_file">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	428 <param name="text_or_file" value="text"/>
16 9a10a6449901 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b iuc parents: 15 diff changeset	429 <param name="accession" value="WP_003249567.1"/>
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	430 </conditional>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	431 <param name="include_flanks_bp" value="100"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	432 </conditional>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	433 <section name="file_choices">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	434 <conditional name="kingdom_cond">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	435 <param name="kingdom_sel" value="prok-gene"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	436 <param name="include" value="gene,protein"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	437 </conditional>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	438 </section>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	439 <output name="gene_data_report">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	440 <assert_contents>
16 9a10a6449901 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b iuc parents: 15 diff changeset	441 <has_text text="WP_003249567.1"/>
9a10a6449901 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b iuc parents: 15 diff changeset	442 <has_text text="menG"/>
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	443 <has_n_lines n="2"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	444 <has_n_columns n="7"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	445 </assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	446 </output>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	447 <output name="gene_fasta">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	448 <assert_contents>
20 35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	449 <has_text text=">"/>
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	450 </assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	451 </output>
16 9a10a6449901 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b iuc parents: 15 diff changeset	452 <output name="gene_flanks">
9a10a6449901 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b iuc parents: 15 diff changeset	453 <assert_contents>
20 35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	454 <has_text text=">"/>
16 9a10a6449901 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b iuc parents: 15 diff changeset	455 </assert_contents>
9a10a6449901 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b iuc parents: 15 diff changeset	456 </output>
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	457 <output name="protein_fasta">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	458 <assert_contents>
20 35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	459 <has_text text=">"/>
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	460 </assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	461 </output>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	462 <assert_command>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	463 <has_text text="include-flanks-bp 100"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	464 </assert_command>
20 35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	465 </test>
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	466 <!-- 10: datasets download gene taxon human -->
16 9a10a6449901 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b iuc parents: 15 diff changeset	467 <!-- <test expect_num_outputs="1">
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	468 <conditional name="query\|subcommand">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	469 <param name="download_by" value="taxon"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	470 <param name="taxon_positional" value="human"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	471 </conditional>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	472 <section name="file_choices">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	473 <conditional name="kingdom_cond">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	474 <param name="include" value=""/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	475 </conditional>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	476 </section>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	477 <output name="gene_data_report">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	478 <assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	479 <has_text text="human"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	480 <has_n_lines min="72000"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	481 <has_n_columns n="8"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	482 </assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	483 </output>
16 9a10a6449901 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b iuc parents: 15 diff changeset	484 </test> -->
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	485 <!-- 11: datasets download gene taxon human + \-\-fasta-filter -->
16 9a10a6449901 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b iuc parents: 15 diff changeset	486 <!-- <test expect_num_outputs="2">
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	487 <conditional name="query\|subcommand">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	488 <param name="download_by" value="taxon"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	489 <param name="taxon_positional" value="human"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	490 </conditional>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	491 <section name="file_choices">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	492 <conditional name="kingdom_cond">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	493 <param name="include" value="protein"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	494 </conditional>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	495 </section>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	496 <section name="filters">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	497 <conditional name="fasta_filter_cond">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	498 <param name="fasta_filter_select" value="text"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	499 <param name="fasta_filter" value="NP_542432.2"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	500 </conditional>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	501 </section>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	502 <output name="gene_data_report">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	503 <assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	504 <has_text text="human"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	505 <has_n_lines min="72000"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	506 <has_n_columns n="8"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	507 </assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	508 </output>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	509 <output name="protein_fasta">
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	510 <assert_contents>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	511 <has_text text=">" n="1" />
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	512 </assert_contents>
16 9a10a6449901 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b iuc parents: 15 diff changeset	513 </output>
9a10a6449901 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 1c7abf3293422fb432b5acd2ef178e7536d65f0b iuc parents: 15 diff changeset	514 </test> -->
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	515 </tests>
20 35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	516 <help><![CDATA[
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	517 .. class:: infomark
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	518
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	519 What it does
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	520
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	521 Downloads gene data from NCBI using the `datasets`_ command-line tool.
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	522 Retrieve gene sequences, transcripts, proteins, and annotation reports.
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	523
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	524 Query Options
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	525
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	526 ============= ================================================================
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	527 Method Description
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	528 ============= ================================================================
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	529 Gene ID NCBI Gene ID (e.g., 672 for BRCA1)
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	530 Symbol Gene symbol with taxon (e.g., TP53 in human)
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	531 Accession RefSeq nucleotide (NM\_) or protein (NP\_/WP\_) accession
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	532 Taxon All genes for a taxon (large downloads)
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	533 ============= ================================================================
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	534
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	535 ----
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	536
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	537 Key Options
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	538
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	539 - Ortholog retrieval: Get orthologous genes across taxa (vertebrates/insects)
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	540 - Taxon filter: Limit WP\_ accession results to specific organisms
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	541 - Flanking sequence: Include nucleotides upstream/downstream (WP\_ only)
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	542 - FASTA filter: Subset output to specific accessions
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	543
20 35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	544 Outputs (Eukaryote)
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	545
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	546 - Gene Data Report: Tabular metadata (ID, symbol, description, coordinates)
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	547 - Gene Product Report: Detailed transcript/protein information
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	548 - Sequences: Gene, RNA, protein, CDS, 5'/3' UTR FASTA files
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	549
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	550 Outputs (Prokaryote)
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	551
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	552 Prokaryotic genes (WP\_ accessions) use a different report format with:
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	553 accession, description, EC number, gene symbol, protein info.
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	554
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	555 Examples
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	556
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	557 Download human BRCA1::
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	558
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	559 Query by: Gene ID
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	560 Gene ID: 672
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	561
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	562 Download TP53 orthologs in rodents::
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	563
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	564 Query by: Symbol
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	565 Symbol: tp53
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	566 Ortholog: rodentia
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	567
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	568
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	569 .. _datasets: https://www.ncbi.nlm.nih.gov/datasets/
35d32c807c23 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb iuc parents: 16 diff changeset	570 ]]></help>
14 a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	571 <expand macro="citations"/>
a222b4d3d52e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit d3fa7b70aa028f527a1dbbb210c172c637dfd4d9 iuc parents: diff changeset	572 </tool>

Mercurial > repos > iuc > ncbi_datasets

annotate datasets_gene.xml @ 20:35d32c807c23 draft default tip