Mercurial > repos > iuc > ncbi_entrez_direct_efetch
diff efetch.xml @ 0:91efba463050 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
| author | iuc |
|---|---|
| date | Tue, 22 Mar 2022 22:30:08 +0000 |
| parents | |
| children | 59dfa639e78e |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/efetch.xml Tue Mar 22 22:30:08 2022 +0000 @@ -0,0 +1,2581 @@ +<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 label="Input File" name="input_file" type="data" format="xml"/> + </when> + <when value="id"> + <param label="Query ID" name="id" type="text" argument="-id"/> + </when> + </conditional> + +<conditional name="db"> + <param name="db" type="select" label="Database" argument="-db"> + <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 name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="assembly"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="bioproject"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="native"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="xml">xml</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="biosample"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="native"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="xml">xml</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="biosystems"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="native"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="xml">xml</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="blastdbinfo"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="books"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="cdd"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="clinvar"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="clone"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="dbvar"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="gap"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="gapplus"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="gds"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="native"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="xml">xml</option> + </param> + </when> + <when value="summary"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="gencoll"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="gene"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="gene_table"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="native"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="asn.1">asn.1</option> + <option value="xml">xml</option> + </param> + </when> + <when value="tabular"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="genome"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="geoprofiles"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="grasp"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="gtr"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="homologene"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="alignmentscores"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="fasta"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="homologene"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="native"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="asn.1">asn.1</option> + <option value="xml">xml</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="medgen"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="mesh"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="native"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="xml">xml</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="ncbisearch"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="nlmcatalog"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="native"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="xml">xml</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="nuccore"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="nucest"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="nucgss"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="nucleotide"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="omim"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="orgtrack"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="pcassay"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="pccompound"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="pcsubstance"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="pmc"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="medline"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="native"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="xml">xml</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="popset"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="probe"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="protein"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="proteinclusters"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="pubmed"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="abstract"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="medline"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="native"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="asn.1">asn.1</option> + <option value="xml">xml</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="pubmedhealth"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="seqannot"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="sequences"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="acc"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="est"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="fasta"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="xml">xml</option> + </param> + </when> + <when value="fasta_cds_aa"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="fasta_cds_na"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="ft"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="gb"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="xml">xml</option> + </param> + </when> + <when value="gbc"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="xml">xml</option> + </param> + </when> + <when value="gbwithparts"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="gene_fasta"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="gp"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="xml">xml</option> + </param> + </when> + <when value="gpc"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="xml">xml</option> + </param> + </when> + <when value="gss"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="ipg"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="xml">xml</option> + </param> + </when> + <when value="native"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="text">text</option> + <option value="xml">xml</option> + </param> + </when> + <when value="seqid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="snp"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="chr"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docset"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="fasta"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="flt"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="native"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="asn.1">asn.1</option> + <option value="xml">xml</option> + </param> + </when> + <when value="rsr"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="ssexemplar"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="sra"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="native"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="xml">xml</option> + </param> + </when> + <when value="runinfo"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="xml">xml</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="structure"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="mmdb"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="native"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="xml">xml</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="taxonomy"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="native"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="xml">xml</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value="unigene"> + <conditional name="format"> + <param name="format" type="select" label="Format" argument="-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 name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="docsum"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + <option value="json">json</option> + </param> + </when> + <when value="full"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="uid"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="url"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + <when value="xml"> + <param name="mode" type="select" label="Mode" argument="-mode"> + <option value="">None</option> + </param> + </when> + </conditional> + </when> + <when value=""> + <param name="db_manual" type="text" label="Database" argument="-db"/> + <param name="format" type="text" label="Format" argument="-format"/> + <param name="mode" type="text" label="Mode" argument="-mode"/> + </when> +</conditional> + + + + + <section name="ranges" title="Set Ranges" expanded="False"> + <param label="Seq Start" name="seq_start" type="integer" optional="True" min="0" argument="-seq_start"/> + <param label="Seq End" name="seq_stop" type="integer" optional="True" min="0" argument="-seq_stop"/> + <param label="strand" name="strand" type="text" argument="-strand"/> + <param label="Complexity" name="complexity" type="integer" optional="True" min="0" argument="-complexity"/> + <param label="Chr Start" name="chr_start" type="integer" optional="True" min="0" argument="-chr_start"/> + <param label="Chr End" name="chr_stop" type="integer" optional="True" min="0" argument="-chr_stop"/> + </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>