<tool id="locarna_pairwise" name="LocARNA Pairwise Aligner" version="@VERSION@.0">
    <description>
        Pairwise Simultaneous Alignment and Folding of RNAs
    </description>

    <macros>
        <import>macros.xml</import>
    </macros>
    
    <expand macro="requirements" />

    <expand macro="stdio" />
    
    <expand macro="version" />
   
    <command><![CDATA[
    #if str($alignment_mode.alignment_mode_selector) == "sparse"
        sparse
    #else
        locarna
    #end if

    '$inputA'
    '$inputB'
    
    --width 60
    
    ## -------------------- alignment mode and specific options

    #if str($alignment_mode.alignment_mode_selector) == "global_locarna"
        #if str($alignment_mode.free_endgaps) != "----"
            --free-endgaps $alignment_mode.free_endgaps
        #end if
    #else if str($alignment_mode.alignment_mode_selector) == "local_locarna"
        --sequ-local on
    #else if str($alignment_mode.alignment_mode_selector) == "structure_local_locarna"
        --struct-local on
    #else if str($alignment_mode.alignment_mode_selector) == "structure_sequence_local_locarna"
        --sequ-local on
        --struct-local on
    #end if

    ## -------------------- scoring parameters
    
    --indel $Scoring.indel
    --indel-opening $Scoring.indel_opening
    --struct-weight $Scoring.struct_weight
    --tau $Scoring.tau
    
    #if str($Scoring.sequence_score.sequence_score_selector) == "match"
        --match $Scoring.sequence_score.match
        --mismatch $Scoring.sequence_score.mismatch
    #else if str($Scoring.sequence_score.sequence_score_selector) == "ribosum"
        --use-ribosum true
    #else if str($Scoring.sequence_score.sequence_score_selector) == "ribofit"
        --ribofit true
    #end if

    ## -------------------- folding parameters

    #if float($Folding.rnafold_temperature) != 37.0
        --rnafold-temperature $Folding.rnafold_temperature
    #end if

    $Folding.alifold_consensus_dp
    --consensus-structure $Folding.consensus_structure

    ## -------------------- heuristic parameters
    
    -p $Heuristics.min_prob
    --max-diff-am $Heuristics.max_diff_am
    --max-diff $Heuristics.max_diff
    --max-diff-at-am $Heuristics.max_diff_at_am
    
    #if float($Heuristics.max_bps_length_ratio) != 0.0
        --max-bps-length-ratio $Heuristics.max_bps_length_ratio
    #end if
    
    ## -------------------- other parameters
        
    $Constraint.lonely_pairs

    #if $Constraint.maxBPspan != -1
        --maxBPspan $Constraint.maxBPspan
    #end if

    $Constraint.ignore_constraints

    ## -------------------- output
    
    #if 'stockholm' in str($outputs).split(",")
        --stockholm '$stockholm'
    #end if
    #if 'clustal' in str($outputs).split(",")
        --clustal '$clustal'
    #end if
    #if 'clustal_strict' in str($outputs).split(",") and (not 'clustal' in str($outputs).split(","))
        --clustal '$clustal_strict'
    #end if
    #if 'pp' in str($outputs).split(",")
        --pp '$pp'
    #end if
    
    $stdout_verbosity

    #if str($stdout_verbosity) != "--quiet":
        > '$stdout'
    #end if

    #if 'clustal' in str($outputs).split(",") and 'clustal_strict' in str($outputs).split(",")
        && cp $clustal $clustal_strict
    #end if

    #if 'clustal_strict' in str($outputs).split(",")
        && sed -i '/\^#/d' '$clustal_strict'
    #end if

    ]]></command>

    <inputs>
        <param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A"
               help="First sequence in fasta, clustal, dp_ps, or PP2.0 format"
               />
        <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B"
               help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"
               />
        <conditional name="alignment_mode">
            <param name="alignment_mode_selector" type="select" label="Alignment mode"
                   help="Note that local alignment mode usually requires to turn off 
                         the 'max-diff' heuristic (maximal difference for alignment traces)."
                   >
                <option value="global_locarna">Global alignment
                (LocARNA)</option>
                <option value="local_locarna">Local alignment (LocARNA)</option>
                <option value="sparse">Global alignment (SPARSE)</option>
                <option value="structure_sequence_local_locarna">
                    Structure and sequence local alignment (LocARNA)
                </option>
                <option value="structure_local_locarna">
                    Structure local, sequence global alignment (LocARNA)
                </option>
            </param>
            <when value="global_locarna">
                <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="----">None</option>
                    <option value="++++">All</option>
                    <option value="+-+-">5' ends</option>
                    <option value="-+-+">3' ends</option>
                    <option value="++--">first sequence</option>
                    <option value="--++">second sequence</option>
                    <option value="+---">sequence A, 5' end</option>
                    <option value="-+--">sequence A, 3' end</option>
                    <option value="--+-">sequence B, 5' end</option>
                    <option value="---+">sequence B, 3' end</option>
                </param>
            </when>
            <when value="local_locarna">
            </when>
            <when value="sparse" />
            <when value="structure_sequence_local_locarna" />
            <when value="structure_local_locarna" />
        </conditional>
        
        <param name="outputs" type="select" display="checkboxes" multiple="True" 
               label="Output options">
            <option value="clustal_strict" selected="True">Output alignment
            in ClustalW format</option>
            <option value="clustal" selected="False">Output alignment
            in constraint-annotated ClustalW format</option>
            <option value="stockholm" selected="False">Output
            alignment in Stockholm format</option>
            <option value="pp" selected="False">Output
            alignment in LocARNA's PP 2.0 format</option>
        </param>
        
        <param name="stdout_verbosity" type="select" label="Standard output verbosity">
            <option value="--quiet">Don't report standard
            output</option>
            <option value="">Non verbose</option>
            <option value="--verbose">Verbose</option>
        </param>
               
        <section name="Scoring" title="Scoring parameters">
            <expand macro="common_scoring_parameters" />
        </section>
        
        <section name="Folding" title="RNA folding parameters">
            <expand macro="common_folding_parameters" />
            <expand macro="alifold_consensus_parameter" />
            <param name="consensus_structure" type="select" label="Consensus structure type"
                   help="Type of consensus structures written to screen and stockholm output"
                   >
                <!-- <option value="mea">mea</option>-->
                <option value="none">none</option>
                <option value="alifold">alifold</option>
            </param>
        </section>

        <section name="Heuristics" title="Heuristic parameters">
            <expand macro="common_heuristic_parameters" />
        </section>

        <section name="Constraint" title="Constraint parameters">
            <expand macro="constraints" />
        </section>
    </inputs>
    
    <outputs>
        <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}">
            <filter>stdout_verbosity != '--quiet'</filter>
        </data>
        <data format="clustal" name="clustal"
              label="${tool.name} alignment (annotated clustal) on ${on_string}">
            <filter>'clustal' in outputs</filter>
        </data>
        <data format="clustal" name="clustal_strict" 
              label="${tool.name} alignment (clustal) on ${on_string}">
            <filter>'clustal_strict' in outputs</filter>
        </data>
        <data format="stockholm" name="stockholm"
              label="${tool.name} alignment (stockholm) on ${on_string}">
            <filter>'stockholm' in outputs</filter>
        </data>
        <data format="txt" name="pp"
              label="${tool.name} alignment (PP 2.0) on ${on_string}">
            <filter>'pp' in outputs</filter>
        </data>
    </outputs>
    
    <tests>
        <test>
            <param name="inputA" value="tRNA_2-1.fa" />
            <param name="inputB" value="tRNA_2-2.fa" />
            <param name="outputs" value="clustal" />
            <output name="clustal" file="tRNA_2.aln" />
        </test>
    </tests>

    <help><![CDATA[ **LocARNA -- Pairwise alignment of RNAs**

Pairwise RNA alignment tools of the LocARNA suite (locarna,
sparse). These tools perform variants of simultaneous RNA folding and
alignment. They can be adapted to specific needs by a broad range of
parameters:

* *scoring* of the alignment, e.g. influencing the cost of
  insertions/deletions and the weight of sequence vs. structure
  similarity.

* *RNA folding*, which control the secondary RNA structure prediciton.

* *heuristics*, which trade alignment accuracy vs. computation
  speed. The huge complexity of simultaneous alignment and folding
  generally requires some heuristics for reasonable computation times.
  Some alignment instances and alignment modes will require relaxation
  of the default heuristics; in particular, local, constrained, and free end gap
  alignment, will often require turning off the "maximal difference for
  alignment traces" heuristic.
  
* *constraints*, which can be applied to include prior knowledge to
  improve the quality of results and/or speed of computation.

**Input.**

Input consists of two sequences or alignments, which are specified in
fasta, clustal, stockholm, or LocARNA pp format.

Optionally, one can specify structure and anchor constraints in these
input files.

**Output.**

The final pairwise alignment is reported in standard and/or variants of the
clustal and stockholm format, as well as LocARNA's own pp format.
    
For more information, see     
.. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
    ]]></help>

    <expand macro="citations" />
    
</tool>