<macros>
    <token name="@VERSION@">1.9.0</token>

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">locarna</requirement>
        </requirements>
    </xml>

    <xml name="stdio">
        <stdio>
            <exit_code range="1:" />
        </stdio>
    </xml>

    <xml name="version">
        <version_command>
            <![CDATA[
                     mlocarna --version
            ]]>
        </version_command>
    </xml>

    <xml name="bed_anchors">
        <conditional name="bed_anchors">
            <param name="bed_anchors_selector" type="select" label="Anchor constraints"
                   help="Anchor constraints in bed format specify positions of
                             named anchor regions per sequence. The sequence names
                             ('contig' names have to correspond to the fasta input
                             sequence names. Anchor names must be unique per sequence
                             and regions of the same name for different sequences
                             must have the same length. This constrains the alignment
                             to align all regions of the same name.">
                <option value="no">Don't load anchor constraints from bed file</option> 
                <option value="yes">Load anchor constraints from bed file</option> 
            </param>
            <when value="no" />
            <when value="yes">
                <param name="bed_anchors_file" type="data" format="tabular" 
                       label="Anchor constraint specification in bed format"
                       />
            </when>
        </conditional>
    </xml>
    
    <xml name="common_scoring_parameters">
        <param name="struct_weight" argument="struct-weight"
               label="Structure weight" type="integer" 
               value="200" min="0" max="800" />
        <param name="indel_opening" argument="indel-opening"
               label="Indel opening score" type="integer"
               value="-500" max="0" min="-1500" />
        <param argument="indel" label="Indel score" type="integer" 
               value="-350" min="-1000" max="0" />
        <param argument="tau" type="integer" value="50"
               min="0" max="200"
               label="Sequence contribution at structure match in percent"/> 

        <conditional name="sequence_score">
            <param name="sequence_score_selector" type="select" label="Type of sequence score contribution">
                <option value="ribofit">Use ribofit</option>
                <option value="ribosum">Use RIBOSUM85_60</option>
                <option value="match">Simple match/mismatch costs</option>
            </param>
            <when value="ribofit" />
            <when value="ribosum" />
            <when value="match">
                <param name="match" type="integer" value="50" 
                       min="0" max="400"
                       label="Match score" />
                <param name="mismatch" type="integer" value="0" 
                       min="-400" max="0"
                       label="Mismatch score" />
            </when>
        </conditional>
    </xml>

    <xml name="plfolding_parameters">
        <param name="plfold_span" argument="--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" argument="--plfold-winsize"
               type="integer" value="300"  min="-1" max="800" 
               label="Window size for local folding" />
    </xml>
    
    <xml name="common_folding_parameters">
        <param name="rnafold_temperature" argument="rnafold-temperature"
               type="float" value="37.0" min="10" max="50"
               label="Temperature for RNAfold (RNAfold's -T option)" />
    </xml>

    <xml name="common_heuristic_parameters">
        <param  name="min_prob" argument="min-prob" type="float" value="0.0005" 
                min="0.0" max="0.2"
                label="Minimal / cutoff probability" /> 

        <param  name="max_diff_am" argument="max-diff-am" 
                type="integer" value="30" 
                min="-1" max="300"
                label="Maximal difference for sizes of matched arcs (-1=off)" /> 

        <param  name="max_diff" argument="max-diff" type="integer"
                value="60" min="-1" max="300"
                label="Maximal difference for alignment traces (-1=off)" /> 

        <param  name="max_diff_at_am" argument="max-diff-am" type="integer" 
                value="-1" min="-1" max="300"
                label="Maximal difference for alignment traces, only at arc match positions" /> 
        
        <param  name="max_bps_length_ratio" argument="max-bps-length-ratio"
                type="float" value="0.0" min="0.0" max="1.0" 
                label="Maximal ratio of #base pairs divided by sequence length (default: no effect)" /> 
    </xml>

    <xml name="alifold_consensus_parameter">
        <param  name="alifold_consensus_dp" argument="alifold-consensus-dp" 
                type="boolean" checked="false" 
                truevalue="--alifold-consensus-dp" falsevalue=""
                label="Compute consensus dot plot by alifold" />
    </xml>
    
    <xml name="constraints">
        <param name="lonely_pairs" type="boolean" truevalue="--LP" falsevalue="--noLP" 
               checked="false" label="Allow lonely base-pairs" help="(--LP/--noLP)" />
        <param name="maxBPspan" argument="--maxBPspan" 
               type="integer" value="-1" min="-1" max="400" 
               label="Maximum basepair span by RNAfold; -1 for arbitrary span" />
        <param name="ignore_constraints" argument="ignore-constraints"
               type="boolean" checked="false" truevalue="--ignore-constraints" falsevalue=""
               help="Ignore all anchor and structure constraints given
                     in the fasta(-ish) input." />
    </xml>

    <xml name="common_other_parameters">
    </xml>

    <xml name="common_outputs">
        <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}">
            <filter>stdout_verbosity != '--quiet'</filter>
        </data>
        <data format="clustal" name="clustal" from_work_dir="mlocarna_results/results/result.aln"
              label="${tool.name} alignment (annotated clustal) on ${on_string}">
            <filter>'clustal' in outputs</filter>
        </data>
        <data format="clustal" name="clustal_strict" 
              from_work_dir="mlocarna_results/results/result.strict-aln"
              label="${tool.name} alignment (clustal) on ${on_string}">
            <filter>'clustal_strict' in outputs</filter>
        </data>
        <data format="stockholm" name="stockholm" from_work_dir="mlocarna_results/results/result.stk"
              label="${tool.name} alignment (stockholm) on ${on_string}">
            <filter>'stockholm' in outputs</filter>
        </data>
        <data format="txt" name="pp"
              from_work_dir="mlocarna_results/results/result.pp"
              label="${tool.name} alignment (PP 2.0) on ${on_string}">
            <filter>'pp' in outputs</filter>
        </data>
        <data format="tar.gz" name="mlocarna_results_tgz"
              label="${tool.name} results archive on ${on_string}">
            <filter>'mlocarna_results' in outputs</filter>
        </data>
    </xml>

    <xml name="citations">
        <citations>
            <citation
            type="doi">10.1371/journal.pcbi.0030065</citation>
            <citation type="doi">10.1261/rna.029041.111</citation>
        </citations>
    </xml>



</macros>