<tool id="cmFinder" name="cmfinder" version="0.3" >
    <requirements>
        <requirement type="package" version="0.5.2">graphclust-wrappers</requirement>
        <requirement type="package" version='0.2'>cmfinder</requirement>
        <requirement type="package" version='2.2.10'>viennarna</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command>
    <![CDATA[

        python '$__tool_directory__/cmFinder.py'
            '$model_tree_stk'
            '$cmfinder_fa'
            ''
            $gap_threshold_opts.gap_threshold_opts_selector
            #if str($gap_threshold_opts.gap_threshold_opts_selector) == '--g':
                $gap_threshold_opts.gap
            #end if
    ]]>
    </command>
    <inputs>
        <param name="model_tree_stk" type="data"  format="stockholm" label="model_tree_stk" help="" />
        <param name="cmfinder_fa" type="data"  format="text" label="cmfinder_fa" help="" />
        <conditional name="gap_threshold_opts">
            <param name="gap_threshold_opts_selector" type="select" label="Use gap threshold" help="">
                <option value="--g" selected="true">Yes (--g)</option>
                <option value="">No</option>
            </param>
            <when value="--g">
                <param name="gap" type="float" value="1.0" size="5"
                        label="Define the gap threshold to determine the conserved column (--g)" help=""/>
            </when>
            <when value=""/>
        </conditional>
    </inputs>
    <outputs>
        <data name="model_cmfinder_stk" format="stockholm" label="model_cmfinder_stk" from_work_dir="model.cmfinder.stk"/>
    </outputs>
    <tests>
        <test>
            <param name="model_tree_stk" value="in.model.tree.stk"/>
            <param name="cmfinder_fa" value="cmfinder.fa"/>
            <param name="gap_threshold_opts.gap_threshold_opts_selector" value="--g"/>
            <param name="gap_threshold_opts.gap" value="1.0"/>
            <output name="model_cmfinder_stk" file="model.cmfinder.stk"/>
        </test>
    </tests>
    <help>
        <![CDATA[
**What it does**

At first it converts CLUSTAL format files to STOCKHOLM format. Then using *CMFinder* determines consensus
motives for sequences.
]]>
    </help>
    <citations>
    <citation type="bibtex">@inproceedings{costa2010fast,
        title={Fast neighborhood subgraph pairwise distance kernel},
        author={Costa, Fabrizio and De Grave, Kurt},
        booktitle={Proceedings of the 26th International Conference on Machine Learning},
        pages={255--262},
        year={2010},
        organization={Omnipress}
      }
      </citation>
      <citation type="doi">10.1093/bioinformatics/btk008</citation>
      <citation type="doi">10.1186/1748-7188-6-26</citation>
  </citations>
</tool>