Mercurial > repos > iuc > ncbi_entrez_direct_esearch
changeset 2:f6046ed1f915 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 1bd7defa5ac7ea1e619c519d719f5bd10452339b
| author | iuc |
|---|---|
| date | Sat, 18 May 2024 20:23:03 +0000 |
| parents | 1033d15d827f |
| children | d75bed16aee8 |
| files | esearch.xml macros.xml |
| diffstat | 2 files changed, 343 insertions(+), 340 deletions(-) [+] |
line wrap: on
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--- a/esearch.xml Sat Dec 17 20:44:51 2022 +0000 +++ b/esearch.xml Sat May 18 20:23:03 2024 +0000 @@ -1,365 +1,368 @@ <tool id="ncbi_entrez_direct_esearch" name="NCBI ESearch" version="@TOOL_VERSION@"> <description>search NCBI Databases by text query</description> <macros> - <import>macros.xml</import> + <import>macros.xml</import> </macros> <expand macro="requirements"/> <version_command>esearch -version</version_command> <command detect_errors="exit_code"><![CDATA[ @ECONTACT@ esearch - -db "${db.db}" - -sort "${db.sort}" - -query "${query}" + -db '${db.db}' + -sort '${db.sort}' + -query '${query}' ${spell} #if $date.constraint: -datetype $date.datetype #if str( $date.days ): - -days "${date.days}" + -days '${date.days}' #end if #if str( $date.mindate ): - -mindate "${date.mindate}" + -mindate '${date.mindate}' #end if #if str( $date.maxdate ): - -maxdate "${date.maxdate}" + -maxdate '${date.maxdate}' #end if #end if > '$output_xml' ]]> </command> - <inputs> - <conditional name="db"> - <param name="db" type="select" label="Choose your DB" 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="snp">snp</option> - <option value="sra">sra</option> - <option value="structure">structure</option> - <option value="taxonomy">taxonomy</option> - <option value="unigene">unigene</option> - </param> - <when value="annotinfo"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="assembly"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="bioproject"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="biosample"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="biosystems"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="blastdbinfo"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="books"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="cdd"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="clinvar"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="clone"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="dbvar"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="gap"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="gapplus"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="gds"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="gencoll"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="gene"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="genome"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="geoprofiles"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="grasp"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="gtr"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="homologene"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="medgen"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="mesh"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> + <inputs> + <conditional name="db"> + <param argument="-db" type="select" label="Choose your 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="snp">snp</option> + <option value="sra">sra</option> + <option value="structure">structure</option> + <option value="taxonomy">taxonomy</option> + <option value="unigene">unigene</option> </param> - </when> - <when value="ncbisearch"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="nlmcatalog"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="nuccore"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="nucest"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="nucgss"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="nucleotide"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="omim"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="orgtrack"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="pcassay"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="pccompound"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="pcsubstance"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="pmc"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="popset"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="probe"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="protein"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="proteinclusters"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> + <when value="annotinfo"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="assembly"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="bioproject"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="biosample"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="biosystems"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="blastdbinfo"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="books"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="cdd"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="clinvar"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="clone"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="dbvar"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="gap"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="gapplus"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="gds"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="gencoll"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="gene"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="genome"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="geoprofiles"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="grasp"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="gtr"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="homologene"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="medgen"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="mesh"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="ncbisearch"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="nlmcatalog"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="nuccore"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="nucest"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="nucgss"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="nucleotide"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="omim"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="orgtrack"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="pcassay"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="pccompound"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="pcsubstance"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="pmc"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="popset"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="probe"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="protein"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="proteinclusters"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="pubmed"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="pubmedhealth"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="seqannot"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="snp"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="sra"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="structure"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="taxonomy"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + <when value="unigene"> + <param argument="-sort" type="select" label="Sort results by"> + <option value="Default Order">Default Order</option> + </param> + </when> + </conditional> + <param argument="-query" type="text" label="Search Term"> + <sanitizer> + <valid> + <add value="'"/> + <add value="["/> + <add value="]"/> + </valid> + </sanitizer> + </param> + <param argument="-spell" type="boolean" truevalue="-spell" falsevalue="" checked="false" label="Correct misspellings in query"/> + <conditional name="date"> + <param name="constraint" type="select" label="Filter By Date"> + <option value="True">Filter by date</option> + <option value="False">Don't filter</option> </param> - </when> - <when value="pubmed"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="pubmedhealth"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="seqannot"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="snp"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="sra"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="structure"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="taxonomy"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - <when value="unigene"> - <param name="sort" type="select" label="Sort results by" argument="-sort"> - <option value="Default Order">Default Order</option> - </param> - </when> - </conditional> - <param label="Search Term" name="query" type="text" argument="-query"> - <sanitizer> - <valid> - <add value="'"/> - <add value="["/> - <add value="]"/> - </valid> - </sanitizer> - </param> - <param name="spell" label="Correct misspellings in query" type="boolean" truevalue="-spell" falsevalue="" checked="false"/> - <conditional name="date"> - <param label="Filter By Date" type="boolean" truevalue="True" falsevalue="False" checked="false" name="constraint"/> - <when value="True"> - <param label="Date type" name="datetype" type="select"> - <option value="PDAT">Publish Date</option> - <option value="EDAT">Entrez Date</option> - <option value="MDAT">Modification Date</option> - </param> - <param label="Number of days in the past" name="days" value="" type="integer" min="1" optional="True"/> - <param label="Minimum date" help="YYYY, YYYY/MM, or YYYY/MM/DD" name="mindate" type="text"/> - <param label="Maximum date" help="YYYY, YYYY/MM, or YYYY/MM/DD" name="maxdate" type="text"/> - </when> - <when value="False"/> - </conditional> - </inputs> - <outputs> - <data format="xml" name="output_xml" label="ESearch Results for $query"/> - </outputs> - <tests> - <test> - <param name="db" value="sra"/> - <param name="query" value="SRP000007"/> - <output name="output_xml"> - <assert_contents> - <has_text_matching expression="ENTREZ_DIRECT" /> - <has_text_matching expression="sra" /> - <has_text_matching expression="WebEnv" /> - <has_text_matching expression="QueryKey" /> - <has_text_matching expression="Count" /> - <has_text_matching expression="Step" /> - <has_text_matching expression="WebEnv" /> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[ + <when value="True"> + <param name="datetype" type="select" label="Date type"> + <option value="PDAT">Publish Date</option> + <option value="EDAT">Entrez Date</option> + <option value="MDAT">Modification Date</option> + </param> + <param name="days" type="integer" min="1" value="" optional="True" label="Number of days in the past"/> + <param name="mindate" type="text" label="Minimum date" help="YYYY, YYYY/MM, or YYYY/MM/DD"/> + <param name="maxdate" type="text" label="Maximum date" help="YYYY, YYYY/MM, or YYYY/MM/DD"/> + </when> + <when value="False"/> + </conditional> + </inputs> + <outputs> + <data format="xml" name="output_xml" label="ESearch Results for $query"/> + </outputs> + <tests> + <test> + <param name="db" value="sra"/> + <param name="query" value="SRP000007"/> + <output name="output_xml"> + <assert_contents> + <has_text_matching expression="ENTREZ_DIRECT"/> + <has_text_matching expression="sra"/> + <has_text_matching expression="WebEnv"/> + <has_text_matching expression="QueryKey"/> + <has_text_matching expression="Count"/> + <has_text_matching expression="Step"/> + <has_text_matching expression="WebEnv"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ NCBI Entrez ESearch =================== @@ -417,5 +420,5 @@ @DISCLAIMER@ ]]></help> - <expand macro="citations"/> + <expand macro="citations"/> </tool>
--- a/macros.xml Sat Dec 17 20:44:51 2022 +0000 +++ b/macros.xml Sat May 18 20:23:03 2024 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">16.2</token> + <token name="@TOOL_VERSION@">21.6</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">entrez-direct</requirement>