annotate epost.xml @ 5:19346cc0c150 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dd9b889d83f058d2ddb87a4e7709ee3d93dddd69"

<?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>