<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_ExtractSbmlAnnot" name="ExtractSbmlAnnot" version="0.12.0">
  <description>Extract databases' references from SBML annotations or notes.</description>
  <xrefs>
    <xref type="bio.tools">met4j</xref>
  </xrefs>
  <requirements>
    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.ExtractSbmlAnnot -i "$inputPath"
 -export "$export"
 -db "$db"
 $uniq
 $skip
 -o "$outputPath"
]]></command>
  <inputs>
    <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
    <param argument="-export" label="the type of entity to extract annotation, either metabolite, reaction, or gene" name="export" optional="false" type="select" value="METABOLITE">
      <option selected="true" value="METABOLITE">METABOLITE</option>
      <option value="REACTION">REACTION</option>
      <option value="GENE">GENE</option>
    </param>
    <param argument="-db" label="name of the referenced database to export annotations from, as listed in notes or identifiers.org base uri" name="db" optional="false" type="text" value="">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param argument="-uniq" checked="false" falsevalue="" label="keep only one identifier if multiple are referenced for the same entity" name="uniq" truevalue="-uniq" type="boolean" value="false"/>
    <param argument="-skip" checked="false" falsevalue="" label="Skip entities without the selected annotations, by default output them with NA value" name="skip" truevalue="-skip" type="boolean" value="false"/>
  </inputs>
  <outputs>
    <data format="tsv" name="outputPath"/>
  </outputs>
  <tests>
    <test>
      <param name="inputPath" value="Human-GEM_pathways.xml"/>
      <param name="export" value="METABOLITE"/>
      <param name="db" value="metanetx.chemical"/>
      <output ftype="tsv" name="outputPath">
      <assert_contents>
        <has_n_lines n="146"/>
        <has_n_columns n="2"/>
      </assert_contents>
    </output>
    </test>
    <test>
      <param name="inputPath" value="Human-GEM_pathways.xml"/>
      <param name="export" value="METABOLITE"/>
      <param name="db" value="metanetx.chemical"/>
      <param name="skip" value="true"/>
      <output ftype="tsv" name="outputPath">
      <assert_contents>
        <has_n_lines n="145"/>
        <has_n_columns n="2"/>
      </assert_contents>
    </output>
    </test>
    <test>
      <param name="inputPath" value="Human-GEM_pathways.xml"/>
      <param name="export" value="METABOLITE"/>
      <param name="db" value="metanetx.chemical"/>
      <param name="skip" value="true"/>
      <param name="uniq" value="true"/>
      <output ftype="tsv" name="outputPath">
      <assert_contents>
        <has_n_lines n="111"/>
        <has_n_columns n="2"/>
      </assert_contents>
    </output>
    </test>
  </tests>
  <help><![CDATA[Extract databases' references from SBML annotations or notes. The references are exported as a tabulated file with one column with the SBML compound, reaction or gene identifiers, and one column with the corresponding database identifier.The name of the targeted database need to be provided under the same form than the one used in the notes field or the identifiers.org uri]]></help>
  <citations/>
</tool>