<tool id="cmFinder" name="CMFinder_v0" version="0.1.0" >
	<requirements>
		<requirement type="package" version="0.1">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>