<?xml version="1.0"?>
<tool id="ncbi_eutils_ecitmatch" name="NCBI ECitMatch" version="@WRAPPER_VERSION@" profile="@PROFILE@">
  <description>search NCBI for citations in PubMed</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <version_command>python ecitmatch.py --version</version_command>
  <command detect_errors="aggressive"><![CDATA[
python '$__tool_directory__/ecitmatch.py'

#if str($input.method) == "file":
    --file $input.citation_file
#else
    #set keys = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
    #set journal_title = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
    #set year = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
    #set volume = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
    #set first_page = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
    #set author = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )

    --key "$keys"
    --journal_title "$journal_title"
    --key "$year"
    --key "$volume"
    --key "$first_page"
    --key "$author"
#end if

@EMAIL_ARGUMENTS@
> $default]]></command>
  <inputs>
    <conditional name="input">
      <param name="method" type="select" label="Input method">
        <option value="file">Load citations from a formatted table</option>
        <option value="direct">Direct Input</option>
      </param>
      <when value="file">
          <param label="Citation table" name="citation_file" type="data"
              format="tabular" help="Columns must be in a specific order, see help documentation"/>
      </when>
      <when value="direct">
        <repeat name="citations" title="Citations">
          <param name="journal_title" type="text" label="Journal Title"
            help="E.g. proc natl acad sci u s a" />
          <param name="year" type="integer" label="Year" value="2000"/>
          <param name="volume" type="integer" label="Volume" value="88"/>
          <param name="first_page" type="integer" label="First Page" value="1"/>
          <param name="author" type="text" label="Author's Name" />
          <param name="key" type="text" label="Citation key"
            help="Used to match input results to NCBI's output" />
        </repeat>
      </when>
    </conditional>

  </inputs>
  <outputs>
    <data format="tabular" name="default" label="ECitMatch Results"/>
  </outputs>
  <tests>
    <test>
      <param name="method" value="file"/>
      <param name="citation_file" value="ecitmatch.tsv"/>
      <output name="default" file="ecitmatch.results.tsv" ftype="tabular"/>
    </test>
  </tests>
  <help><![CDATA[
NCBI ECitMatch
==============

Search for citation PubMed IDs. These can be provided via a tabular file, or
via direct input. If provided via file, the columns should be ordered:

1. Journal Name
2. Year
3. Volume
4. First Page
5. Author Name
6. Citation Key


An example query:

+---------------+--------------------------+
| Parameter     | Value                    |
+===============+==========================+
| Journal Title | proc natl acad sci u s a |
+---------------+--------------------------+
| Year          | 1991                     |
+---------------+--------------------------+
| Volume        | 88                       |
+---------------+--------------------------+
| First Page    | 3248                     |
+---------------+--------------------------+
| Author Name   | mann bj                  |
+---------------+--------------------------+
| Citation Key  | citation_1               |
+---------------+--------------------------+


@REFERENCES@

@DISCLAIMER@
      ]]></help>
  <expand macro="citations"/>
</tool>