<macros>
    <token name="@TOOL_VERSION@">1.1.1</token>
    <token name="@HELP@">More information can be found at https://github.com/ebi-gene-expression-group/cell-types-analysis</token>
    <token name="@PROFILE@">18.01</token>
    <xml name="requirements">
      <requirements>
        <requirement type="package" version="0.1.9">cell-types-analysis</requirement>
            <yield/>
      </requirements>
    </xml>
    <xml name="version">
      <version_command><![CDATA[
        conda list | grep cell-types-analysis | egrep -o [0-9]\.[0-9]\.[0-9]
    ]]></version_command>
    </xml>
    <token name="@VERSION_HISTORY@"><![CDATA[
**Version history**
0.1.6+galaxy0: Add removing non-alphanumeric characters from labels in metadata files
0.0.5+galaxy0: Initial contribution. Andrey Solovyev, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/.
0.0.5+galaxy1: Standardise input/output format into .txt. 
    ]]></token>
    <xml name="sem_siml_options">
      <param type="select" name="sem_siml_metric" label="Semantic similarity metric"  help="What semantic similarity metric should be used? NB: if include-sem-siml is set to True, make sure to use a metric that is in the [0;1] interval. See https://www.bioconductor.org/packages/release/bioc/html/Onassis.html for more detail.">
            <option value="lin" selected="true">lin</option>
            <option value="jaccard">jaccard</option>
            <option value="jc_norm">jc_norm</option>
            <option value="schlicker">schlicker</option>
            <option value="edge_resnik">edge_resnik</option>
            <option value="sim">sim</option>
            <option value="edge_leachod">edge_leachod</option>
            <option value="edge_slimani">edge_slimani</option>
            <option value="edge_wupalmer">edge_wupalmer</option>
            <option value="edge_rada_lca">edge_rada_lca</option>
            <option value="edge_li">edge_li</option>
            <option value="resnik">resnik</option>
        </param>
    </xml>
    <xml name="sanitize_strings">
        <sanitizer invalid_char="">
        <valid initial="string.ascii_letters,string.digits">
            <add value="_" />
            <add value="-" />
            <add value="[" />
            <add value="]" />
            <add value=" " />
            </valid>
    </sanitizer>
    </xml>
    <xml name="citations">
      <citations>
        <citation type="bibtex">
          @misc{github-cell-types-analysis.git,
            author = {Andrey Solovyev, EBI Gene Expression Team},
            year = {2020},
            title = {Suite of scripts for analysis of scRNA-seq cell type classification tool outputs},
            publisher = {GitHub},
            journal = {GitHub repository},
            url = {https://github.com/ebi-gene-expression-group/cell-types-analysis.git},
          }
        </citation>
        <citation type="doi">10.1101/2020.04.08.032698</citation>
        <yield />
      </citations>
    </xml>
</macros>