Mercurial > repos > iuc > ncbi_eutils_esearch
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
author | iuc |
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date | Tue, 30 Oct 2018 19:08:02 -0400 |
parents | c8a84e910e6b |
children | c6096cd97120 |
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<?xml version="1.0"?> <tool id="ncbi_eutils_esearch" name="NCBI ESearch" version="@WRAPPER_VERSION@"> <description>search NCBI Databases by text query</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <version_command>python esearch.py --version</version_command> <command detect_errors="aggressive" interpreter="python"><![CDATA[ esearch.py $db_select "$term" #if $history_file and $history_file is not None: --history_file '$history_file' #end if #if $date.enabled == 'True' --datetype $date.datetype #if $date.reldate and $date.reldate is not None: --reldate $date.reldate #end if #if $date.mindate and $date.mindate is not None: --mindate '$date.mindate' #end if #if $date.maxdate and $date.maxdate is not None: --maxdate '$date.maxdate' #end if #end if #if $use_history: --history_out $history #end if @EMAIL_ARGUMENTS@ > $default]]></command> <inputs> <expand macro="dbselect"/> <param name="term" type="text" label="Search term"> <sanitizer> <valid> <add value="'"/> <add value="["/> <add value="]"/> </valid> </sanitizer> </param> <param name="history_file" type="data" format="json" optional="true" label="Filter existing history" /> <param name="use_history" type="boolean" truevalue="--use_history" falsevalue="" checked="false" label="Store results to history server" /> <conditional name="date"> <param name="enabled" type="select" label="Filter by date"> <option value="False">No</option> <option value="True">Yes</option> </param> <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 name="reldate" type="integer" min="1" optional="true" label="In past N days" /> <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 name="default" format="json" label="ESearch results for $term"> <change_format> <when input="use_history" value="" format="xml"/> </change_format> </data> <expand macro="history_out"> <filter>use_history</filter> </expand> </outputs> <tests> <test> <param name="db_select" value="pubmed"/> <param name="term" value="(PNAS[ta] AND 97[vi])"/> <output name="default" file="esearch.pubmed.xml" ftype="xml" lines_diff="2"/> </test> <test> <param name="db_select" value="pubmed"/> <param name="term" value="PNAS[ta]"/> <param name="enabled" value="True"/> <param name="datetype" value="PDAT"/> <param name="mindate" value="2014/01/01"/> <param name="maxdate" value="2014/02/01"/> <output name="default" file="esearch.pubmed.2014-01-pnas.xml" ftype="xml" lines_diff="2"/> </test> </tests> <help><![CDATA[ NCBI Entrez ESearch =================== Responds to a text query with the list of matching UIDs in a given database (for later use in ESummary, EFetch or ELink), along with the term translations of the query. Example Queries --------------- Search in PubMed with the term cancer for abstracts that have an Entrez date within the last 60 days: +----------------------+-------------+ | Parameter | Value | +======================+=============+ | NCBI Database to Use | PubMed | +----------------------+-------------+ | Term | Cancer | +----------------------+-------------+ | Datetype | Entrez Date | +----------------------+-------------+ | In past N Days | 60 | +----------------------+-------------+ Search PubMed Central for free full text articles containing the query stem cells: +----------------------+--------------------------------------+ | Parameter | Value | +======================+======================================+ | NCBI Database to Use | PubMedCentral | +----------------------+--------------------------------------+ | Term | Stem Cells AND free fulltext[filter] | +----------------------+--------------------------------------+ Search in Nucleotide for all tRNAs: +----------------------+--------------------------------------+ | Parameter | Value | +======================+======================================+ | NCBI Database to Use | Nucleotide | +----------------------+--------------------------------------+ | Term | biomol trna[prop] | +----------------------+--------------------------------------+ Search in Protein for a molecular weight range: +----------------------+--------------------------------------+ | Parameter | Value | +======================+======================================+ | NCBI Database to Use | Protein | +----------------------+--------------------------------------+ | Term | 70000:90000[molecular weight] | +----------------------+--------------------------------------+ @REFERENCES@ @DISCLAIMER@ ]]></help> <expand macro="citations"/> </tool>