<tool id="locarna_best_subtree" name="locarna_graphclust" version="0.3" >
  <requirements>
    <requirement type="package" version="0.5.2">graphclust-wrappers</requirement>
    <requirement type="package" version='1.8.10'>locarna</requirement>
    <requirement type="package" version='2.1'>rnaz</requirement>
    <requirement type="package" version='0.07'>perl-math-round</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" />
  </stdio>
  <command>
    <![CDATA[

        locARNAGraphClust.pl
            '$center_fa_file'
            '$tree_file'
            '$tree_matrix'
            '$data_map'
            $allow_overlap
            $free_endgaps

        #if str($param_type.param_type_selector) == "gclust"
            $param_type.p
            $param_type.max_diff_am
            $param_type.max_diff
            $param_type.tau
            $param_type.plfold_minlen
            $param_type.struct_weight
            $param_type.indel_opening
            $param_type.indel
            $param_type.alifold_consensus_dp
            $param_type.plfold_span
            $param_type.plfold_winsize
         #end if
        ]]>
  </command>
  <inputs>
    <param type="data" name="center_fa_file" label="centers" format="fa, fasta" help="fasta format" />
    <param type="data" name="tree_file" label="trees" format="text" help="text format" />
    <param type="data" name="tree_matrix" label="tree_matrix" format="text" help="text format" />
    <param type="data" name="data_map" label="data_map" format="txt" help="text format" />
    <param name="allow_overlap" type="boolean"  truevalue="1" falsevalue="0" label="Allow overlap in subtrees" help="otherwise ignore subtree if it contains overlapping sequences"/>

    <param name="free_endgaps" type="select" label="Free endgaps"
            help="Specify whether gaps at the ends (all, 5', or 3' ends)
                  of the sequences should be penalized or allowed for free.">
        <option value="0">No free endgaps</option>
        <option value="--free-endgaps">Free endgaps</option>
        <option value="--free-endgaps-5">Free endgaps, only 5'</option>
        <option value="--free-endgaps-3">Free endgaps, only 3'</option>
    </param>
    <conditional name="param_type">
        <param name="param_type_selector" type="select" label="Choose the type of parameters">
            <option value="locarna">LocARNA defaults</option>
            <option value="gclust" selected="True">GrapClust defaults(changeable)</option>
        </param>
        <when value="gclust">
          <param name="p" type="float" value="0.001" size="5" label="minimal probability" help="-p"/>
          <param name="max_diff_am" type="integer" value="50" size="5" label=" maximal difference for sizes of matched arcs" help="--max-diff-am"/>
          <param argument="tau" type="integer" value="50" min="0" max="200" label="Sequence contribution at structure match in percent"/>
          <param name="max_diff" type="integer" value="100" size="5" label="maximal difference for alignment traces" help="--max-diff"/>
          <param name="plfold_minlen" type="integer" value="210" size="5" label="Minimal length of a sequences for which RNAplfold is used" />
          <param name="struct_weight" argument="struct-weight"
                  label="Structure weight" type="integer"
                  value="180" min="0" max="800" />
          <param name="indel_opening" argument="indel-opening"
                  label="Indel opening score" type="integer"
                  value="-400" max="0" min="-1500" />
          <param argument="indel" label="Indel score" type="integer"
                  value="-200" min="-1000" max="0" />
          <param  name="alifold_consensus_dp"
                   type="boolean" checked="True"
                   truevalue="--alifold-consensus-dp" falsevalue=" "
                   label="Compute consensus dot plot by alifold" />
          <param name="plfold_span"
                    type="integer" value="150" min="-1" max="400"
                    label="Maximum basepair span by RNAplfold (local folding); -1 for global folding" />
          <param name="plfold_winsize"
                type="integer" value="300"  min="-1" max="800"
                label="Window size for local folding" />
        </when>
        <when value="locarna" />
    </conditional>
    </inputs>
    <outputs>
        <data name="model_tree_stk" format="stockholm" label="model.tree.stk" from_work_dir="MODEL/best_subtree.aln" />
    </outputs>
    <tests>
        <test>
            <param name="tree_file" value="1.1.tree"/>
            <param name="center_fa_file" value="1.1.center.fa"/>
            <param name="data_map" value="data.map"/>
            <param name="tree_matrix" value="1.1.matrix.tree"/>
            <param name="allow_overlap" value="0"/>
            <param name="free_endgaps" value="0"/>
            <param name="param_type_selector" value="gclust"/>
            <param name="p" value="0.001"/>
            <param name="max_diff_am" value="50"/>
            <param name="tau" value="50"/>
            <param name="max_diff" value="100"/>
            <param name="plfold_minlen" value="210"/>
            <param name="struct_weight" value="180"/>
            <param name="indel_opening" value="-400"/>
            <param name="indel" value="-200"/>
            <param name="alifold_consensus_dp" value="--alifold-consensus-dp"/>
            <param name="plfold_span" value="150"/>
            <param name="plfold_winsize" value="300"/>
            <output name="model_tree_stk" file="best_subtree.aln"/>
        </test>
    </tests>
    <help>
    <![CDATA[
**What it does**

MLocARNA computes a multiple sequence-structure alignment of RNA sequences.
It uses *treefile* - file with guide tree in NEWICK format. The given tree is used as guide tree for the progressive alignment.
This saves the calculation of pairwise all-vs-all similarities and construction of the guide tree.


]]>
  </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">10.1261/rna.029041.111</citation>
      <citation type="doi">10.1371/journal.pcbi.0030065</citation>
      <citation type="doi">10.1093/nar/gkq316</citation>
  </citations>
</tool>