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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 1f7b04db717bd82f93519fdc3f34f589bb671e48
author | iuc |
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date | Mon, 29 Jul 2024 07:07:23 +0000 |
parents | 59dfa639e78e |
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<tool id="ncbi_entrez_direct_efetch" name="NCBI EFetch" version="@TOOL_VERSION@"> <description>fetch records from NCBI</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <version_command>efetch -version</version_command> <command detect_errors="exit_code"><![CDATA[ @ECONTACT@ efetch #if str( $db.db ) == "": #if str( $db.db_manual ): -db "${db.db_manual}" #end if #if str( $db.format ): -format "${db.format}" #end if #if str( $db.mode ): -mode "${db.mode}" #end if #else: #if str( $db.db ): -db "${db.db}" #end if #if str( $db.format.format ): -format "${db.format.format}" #end if #if str( $db.format.mode ): -mode "${db.format.mode}" #end if #end if #if str( $ranges.seq_start ): -seq_start "${ranges.seq_start}" #end if #if str( $ranges.seq_stop ): -seq_stop "${ranges.seq_stop}" #end if #if str( $ranges.strand ): -strand "${ranges.strand}" #end if #if str( $ranges.complexity ): -complexity "${ranges.complexity}" #end if #if str( $ranges.chr_start ): -chr_start "${ranges.chr_start}" #end if #if str( $ranges.chr_stop ): -chr_stop "${ranges.chr_stop}" #end if #if str( $query.source ) == "id": -id "${query.id}" #else: < '$query.input_file' #end if > '${output_result}' ]]> </command> <inputs> <conditional name="query"> <param name="source" type="select" label="Select query source"> <option value="history">NCBI WebEnv History</option> <option value="id">Direct Entry</option> </param> <when value="history"> <param name="input_file" type="data" format="xml" label="Input File"/> </when> <when value="id"> <param argument="-id" type="text" label="Query ID"/> </when> </conditional> <conditional name="db"> <param argument="-db" type="select" label="Database"> <option value="annotinfo">annotinfo</option> <option value="assembly">assembly</option> <option value="bioproject">bioproject</option> <option value="biosample">biosample</option> <option value="biosystems">biosystems</option> <option value="blastdbinfo">blastdbinfo</option> <option value="books">books</option> <option value="cdd">cdd</option> <option value="clinvar">clinvar</option> <option value="clone">clone</option> <option value="dbvar">dbvar</option> <option value="gap">gap</option> <option value="gapplus">gapplus</option> <option value="gds">gds</option> <option value="gencoll">gencoll</option> <option value="gene">gene</option> <option value="genome">genome</option> <option value="geoprofiles">geoprofiles</option> <option value="grasp">grasp</option> <option value="gtr">gtr</option> <option value="homologene">homologene</option> <option value="medgen">medgen</option> <option value="mesh">mesh</option> <option value="ncbisearch">ncbisearch</option> <option value="nlmcatalog">nlmcatalog</option> <option value="nuccore">nuccore</option> <option value="nucest">nucest</option> <option value="nucgss">nucgss</option> <option value="nucleotide">nucleotide</option> <option value="omim">omim</option> <option value="orgtrack">orgtrack</option> <option value="pcassay">pcassay</option> <option value="pccompound">pccompound</option> <option value="pcsubstance">pcsubstance</option> <option value="pmc">pmc</option> <option value="popset">popset</option> <option value="probe">probe</option> <option value="protein">protein</option> <option value="proteinclusters">proteinclusters</option> <option value="pubmed">pubmed</option> <option value="pubmedhealth">pubmedhealth</option> <option value="seqannot">seqannot</option> <option value="sequences">sequences</option> <option value="snp">snp</option> <option value="sra">sra</option> <option value="structure">structure</option> <option value="taxonomy">taxonomy</option> <option value="unigene">unigene</option> <option value="">Manual Entry</option> </param> <when value="annotinfo"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="assembly"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="bioproject"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="native">native</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="native"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="xml">xml</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="biosample"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="native">native</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="native"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="xml">xml</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="biosystems"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="native">native</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="native"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="xml">xml</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="blastdbinfo"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="books"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="cdd"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="clinvar"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="clone"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="dbvar"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="gap"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="gapplus"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="gds"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="native">native</option> <option value="summary">summary</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="native"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="xml">xml</option> </param> </when> <when value="summary"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="gencoll"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="gene"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="gene_table">gene_table</option> <option value="native">native</option> <option value="tabular">tabular</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="gene_table"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="native"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="asn.1">asn.1</option> <option value="xml">xml</option> </param> </when> <when value="tabular"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="genome"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="geoprofiles"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="grasp"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="gtr"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="homologene"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="alignmentscores">alignmentscores</option> <option value="docsum">docsum</option> <option value="fasta">fasta</option> <option value="full">full</option> <option value="homologene">homologene</option> <option value="native">native</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="alignmentscores"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="fasta"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="homologene"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="native"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="asn.1">asn.1</option> <option value="xml">xml</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="medgen"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="mesh"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="native">native</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="native"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="xml">xml</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="ncbisearch"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="nlmcatalog"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="native">native</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="native"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="xml">xml</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="nuccore"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="nucest"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="nucgss"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="nucleotide"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="omim"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="orgtrack"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="pcassay"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="pccompound"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="pcsubstance"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="pmc"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="medline">medline</option> <option value="native">native</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="medline"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="native"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="xml">xml</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="popset"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="probe"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="protein"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="proteinclusters"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="pubmed"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="abstract">abstract</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="medline">medline</option> <option value="native">native</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="abstract"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="medline"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="native"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="asn.1">asn.1</option> <option value="xml">xml</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="pubmedhealth"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="seqannot"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="sequences"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="acc">acc</option> <option value="docsum">docsum</option> <option value="est">est</option> <option value="fasta">fasta</option> <option value="fasta_cds_aa">fasta_cds_aa</option> <option value="fasta_cds_na">fasta_cds_na</option> <option value="ft">ft</option> <option value="full">full</option> <option value="gb">gb</option> <option value="gbc">gbc</option> <option value="gbwithparts">gbwithparts</option> <option value="gene_fasta">gene_fasta</option> <option value="gp">gp</option> <option value="gpc">gpc</option> <option value="gss">gss</option> <option value="ipg">ipg</option> <option value="native">native</option> <option value="seqid">seqid</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="acc"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="est"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="fasta"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="xml">xml</option> </param> </when> <when value="fasta_cds_aa"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="fasta_cds_na"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="ft"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="gb"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="xml">xml</option> </param> </when> <when value="gbc"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="xml">xml</option> </param> </when> <when value="gbwithparts"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="gene_fasta"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="gp"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="xml">xml</option> </param> </when> <when value="gpc"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="xml">xml</option> </param> </when> <when value="gss"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="ipg"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="xml">xml</option> </param> </when> <when value="native"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="text">text</option> <option value="xml">xml</option> </param> </when> <when value="seqid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="snp"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="chr">chr</option> <option value="docset">docset</option> <option value="docsum">docsum</option> <option value="fasta">fasta</option> <option value="flt">flt</option> <option value="full">full</option> <option value="native">native</option> <option value="rsr">rsr</option> <option value="ssexemplar">ssexemplar</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="chr"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docset"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="fasta"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="flt"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="native"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="asn.1">asn.1</option> <option value="xml">xml</option> </param> </when> <when value="rsr"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="ssexemplar"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="sra"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="native">native</option> <option value="runinfo">runinfo</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="native"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="xml">xml</option> </param> </when> <when value="runinfo"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="xml">xml</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="structure"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="mmdb">mmdb</option> <option value="native">native</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="mmdb"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="native"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="xml">xml</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="taxonomy"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="native">native</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="native"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="xml">xml</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value="unigene"> <conditional name="format"> <param argument="-format" type="select" label="Format"> <option value="">None</option> <option value="docsum">docsum</option> <option value="full">full</option> <option value="uid">uid</option> <option value="url">url</option> <option value="xml">xml</option> </param> <when value=""> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="docsum"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> <option value="json">json</option> </param> </when> <when value="full"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="uid"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="url"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> <when value="xml"> <param argument="-mode" type="select" label="Mode"> <option value="">None</option> </param> </when> </conditional> </when> <when value=""> <param name="db_manual" argument="-db" type="text" label="Database"/> <param argument="-format" type="text" label="Format"/> <param argument="-mode" type="text" label="Mode"/> </when> </conditional> <section name="ranges" title="Set Ranges" expanded="False"> <param argument="-seq_start" type="integer" min="0" optional="True" label="Seq Start"/> <param argument="-seq_stop" type="integer" min="0" optional="True" label="Seq End"/> <param argument="-strand" type="text" label="strand"/> <param argument="-complexity" type="integer" min="0" optional="True" label="Complexity"/> <param argument="-chr_start" type="integer" min="0" optional="True" label="Chr Start"/> <param argument="-chr_stop" type="integer" min="0" optional="True" label="Chr End"/> </section> </inputs> <outputs> <data format="txt" name="output_result"> <change_format> <when input="db.format" value="xml" format="xml"/> <when input="db.format.mode" value="xml" format="xml"/> <when input="db.format.mode" value="json" format="json"/> <when input="db.format" value="tabular" format="tabular"/> <when input="db.format" value="fasta" format="fasta"/> <when input="db.format" value="fasta_cds_aa" format="fasta"/> <when input="db.format" value="fasta_cds_na" format="fasta"/> <when input="db.format" value="gene_fasta" format="fasta"/> </change_format> </data> </outputs> <tests> <test> <param name="db|db" value=""/> <param name="db|db_manual" value="sra"/> <param name="db|format" value="runinfo"/> <param name="query|source" value="id"/> <param name="query|id" value="SRX8542266"/> <output name="output_result"> <assert_contents> <has_text_matching expression="Run"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ NCBI Entrez EFetch ================== Responds to a list of UIDs in a given database with the corresponding data records in a specified format. Example Queries --------------- Fetch PMIDs 17284678 and 9997 as text abstracts: +----------------------+--------------------------------------+ | Parameter | Value | +======================+======================================+ | NCBI Database to Use | PubMed | +----------------------+--------------------------------------+ | ID List | 17284678 9997 | +----------------------+--------------------------------------+ | Output Format | Abstract | +----------------------+--------------------------------------+ Fetch FASTA for a transcript and its protein product (GIs 312836839 and 34577063) +----------------------+--------------------------------------+ | Parameter | Value | +======================+======================================+ | NCBI Database to Use | Protein | +----------------------+--------------------------------------+ | ID List | 312836839 34577063 | +----------------------+--------------------------------------+ | Output Format | Fasta | +----------------------+--------------------------------------+ @DISCLAIMER@ ]]></help> <expand macro="citations"/> </tool>