Mercurial > repos > iuc > ncbi_eutils_epost
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dd9b889d83f058d2ddb87a4e7709ee3d93dddd69"
author | iuc |
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date | Fri, 27 Aug 2021 11:27:58 +0000 |
parents | ae3a5d753d42 |
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<?xml version="1.0"?> <tool id="ncbi_eutils_epost" name="NCBI EPost" version="@WRAPPER_VERSION@" profile="@PROFILE@"> <description>post UIDs to NCBI History Server</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <version_command>python epost.py --version</version_command> <command detect_errors="aggressive"> <![CDATA[ python '$__tool_directory__/epost.py' $db_select @EMAIL_ARGUMENTS@ #if $query_source.qss == "id_file": --id_list $query_source.id_file #else if $query_source.qss == "id_list": --id $query_source.id_list #else if $query_source.qss == "id_xml": --id_xml $query_source.id_xml #else if $query_source.qss == "id_json": --id_json $query_source.id_json #end if #if $update_history.history_type == "select" and $update_history.history_entry.history_select == "history_json": --history_file "$update_history.history_entry.history_file" #else if $update_history.history_type == "select" and $update_history.history_entry.history_select == "history_xml": --history_xml "$update_history.history_entry.history_xml" #else if $update_history.history_type == "paste": --webenv "$update_history.webenv" #end if > $history ]]> </command> <inputs> <conditional name="query_source"> <param name="qss" type="select" label="Enter Query IDs by..." help="Files output by ELink or ESearch are acceptable. Query IDs in an ELink result are ignored."> <option value="id_file" selected="True">ID file (Tabular)</option> <option value="id_xml">ID File (XML)</option> <option value="id_json">ID File (JSON)</option> <option value="id_list">Paste IDs</option> </param> <when value="id_file"> <param label="ID File (Text)" name="id_file" type="data" format="text,tabular" help="A Text file containing one ID per line"/> </when> <when value="id_xml"> <param label="ID File (XML)" name="id_xml" type="data" format="xml" help="ESearch or ELink Result XML file"/> </when> <when value="id_json"> <param label="ID File (JSON)" name="id_json" type="data" format="json" help="ESearch or ELink Result JSON file"/> </when> <when value="id_list"> <param label="Paste ID List" name="id_list" type="text" area="true" help="Newline/Comma separated list of IDs"/> </when> </conditional> <expand macro="dbselect"/> <conditional name="update_history"> <param name="history_type" type="select" label="Target History" help="IDs will be saved to a supplied or created history."> <option value="create" selected="True">Create a new history</option> <option value="select">Add to an existing history by file</option> <option value="paste">Add to an existing history by history (WebEnv) ID</option> </param> <when value="create"/> <when value="select"> <conditional name="history_entry"> <param name="history_select" type="select" label="Select an existing history"> <option value="history_json">History File (JSON)</option> <option value="history_xml">History File (XML)</option> </param> <when value="history_json"> <param label="History File (JSON)" name="history_file" type="data" format="json" help="A JSON file containing the WebEnv ID referencing the history on the NCBI history server to which to add the IDs"/> </when> <when value="history_xml"> <param label="History File (XML)" name="history_xml" type="data" format="xml" help="An XML file containing the WebEnv ID referencing the history on the NCBI history server to which to add the IDs"/> </when> </conditional> </when> <when value="paste"> <param name="webenv" type="text" label="WebEnv History ID"/> </when> </conditional> </inputs> <outputs> <data format="json" name="history" label="NCBI History"/> </outputs> <tests> <test> <param name="db_select" value="nuccore"/> <param name="qss" value="id_list"/> <param name="id_list" value="126697566"/> <param name="history_type" value="create"/> <output name="history" file="example.history.json" compare="sim_size" delta="70" ftype="json"/> </test> </tests> <help><![CDATA[ NCBI Entrez EPost ================= Accepts a list of UIDs from a given database, stores the set on the History Server, and responds with an NCBI History reference. @REFERENCES@ @DISCLAIMER@ ]]></help> <expand macro="citations"/> </tool>