<tool id="locarna_exparnap" name="LocARNA Exact Matcher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>
        Pairwise Simultaneous Matching and Folding of RNAs (ExpaRNA-P)
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version"/>
    <command><![CDATA[
    exparna_p
    '$inputA'
    '$inputB'

    ## -------------------- scoring parameters -------------#
    $Scoring.no_stacking
    --alpha_1 $Scoring.alpha_1
    --alpha_2 $Scoring.alpha_2
    --alpha_3 $Scoring.alpha_3
    --struct-mismatch-score $Scoring.struct_mismatch_score

    @HEURISTIC_ARGS@
    --max-uil-length-ratio $Heuristics.max_uil_length_ratio
    --max-bpil-length-ratio $Heuristics.max_bpil_length_ratio
    --prob_unpaired_in_loop_threshold $Heuristics.prob_unpaired_in_loop_threshold
    --prob_basepair_in_loop_threshold $Heuristics.prob_basepair_in_loop_threshold

    @CONSTRAINT_ARGS@
    @FOLDING_ARGS@
    ## -------------------- other parameters---------------- #
    #if str($Other.subopt.subopt_selector) == "on"
        --diff-to-opt-score $Other.subopt.diff_to_opt_score
        --number-of-EPMs $Other.subopt.number_of_EPMs
    #end if

    --min-score $Other.min_score

    $Other.inexact_struct_match
    $Other.add_filter
    $Other.no_chaining
    --out-min-prob $Other.out_min_prob

    ## -------------------- output ---------------- #

    #if 'postscript' in str($outputs).split(",")
        --output-ps
        --PS_fileA '$ps_fileA'
        --PS_fileB '$ps_fileB'
    #end if

    #if 'anchors-fasta' in str($outputs).split(",")
        --output-locarna '$anchors_fasta'
    #end if

    #if 'anchors-pp' in str($outputs).split(",")
        --output-anchor-pp anchors_pp
    #end if

    #if 'clustal' in str($outputs).split(",")
        --output-clustal '$clustal'
    #end if

    #if 'epm_list' in str($outputs).split(",")
        --output-epm-list '$epm_list'
    #end if

    #if 'chained_epm_list' in str($outputs).split(",")
        --output-chained-epm-list '$chained_epm_list'
    #end if

    @STDOUT_ARGS@

    ## -------------------- post processing --------------#

    #if 'anchors-pp' in str($outputs).split(",")
        && mv anchors_pp_A.pp '$anchors_ppA'
        && mv anchors_pp_B.pp '$anchors_ppB'
    #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"/>
        <param name="outputs" type="select" display="checkboxes" multiple="true" label="Output options">
            <option value="postscript" selected="false">Best EPM chain as colored postscript</option>
            <option value="anchors-fasta" selected="false">Fasta with anchor constraints from chaining</option>
            <option value="anchors-pp" selected="false">LocARNA PP files merging input PPs and anchor constraints from chaining</option>
            <option value="clustal" selected="false">Chain as alignment in Clustal format</option>
            <option value="epm_list" selected="false">List of the found EPMs</option>
            <option value="chained_epm_list" selected="false">List of EPMs in the best chain</option>
        </param>
        <param name="stdout_verbosity" type="select" label="Standard output verbosity">
            <option value="--quiet">Don't report standard output</option>
            <option value="" selected="true">Non verbose</option>
            <option value="--verbose">Verbose</option>
        </param>
        <section name="Scoring" title="Scoring parameters">
            <param argument="--alpha_1" type="integer" value="1" min="0" max="50" label="Sequence score factor"/>
            <param argument="--alpha_2" type="integer" value="5" min="0" max="50" label="Structure score factor"/>
            <param argument="--no-stacking" type="boolean" truevalue="" falsevalue="--no-stacking" label="Add stacking terms"/>
            <param argument="--alpha_3" type="integer" value="5" min="0" max="50" label="Stacking score factor"/>
            <param argument="--struct-mismatch-score" type="integer" value="-10" min="-100" max="0" label="Score for nucleotide mismatch in base pair match"/>
        </section>
        <section name="Folding" title="RNA folding parameters">
            <expand macro="common_folding_parameters" />
        </section>
        <section name="Heuristics" title="Heuristic parameters">
            <expand macro="common_heuristic_parameters" />
            <expand macro="max_diff_parameters" />
            <expand macro="in_loop_ratio_parameters" />
            <expand macro="exparnap_in_loop_parameters" />
        </section>
        <section name="Constraints" title="Constraint parameters">
            <expand macro="common_constraint_parameters" />
        </section>
        <section name="Other" title="Other parameters">
            <conditional name="subopt">
                <param name="subopt_selector" type="select" label="Suboptimal traceback of EPMs (exact pattern matches)" help="(--subopt)">
                    <option value="off">Enumerate only optimal EPMs</option>
                    <option value="on">Perform suboptimal traceback of EPMs</option>
                </param>
                <when value="off" />
                <when value="on">
                    <param argument="--diff-to-opt-score" type="integer" value="-1" min="-20" max="0" label="Maximum score difference to optimum" />
                    <param argument="--number-of-EPMs" type="integer" value="100" min="1" max="10000" label="Maximal number of EPMs" />
                </when>
            </conditional>

            <param argument="--min-score" type="integer" value="30" min="0" max="1000" label="Minimum score of EPM" />
            <param argument="--inexact-struct-match" type="boolean" truevalue="--inexact-struct-match" falsevalue="" label="Allow inexact structure matches"/>
            <param argument="--add-filter" type="boolean" truevalue="--add-filter" falsevalue="" checked="false" label="Apply an additional filter to enumerate only EPMs that are maximally extended (only inexact)"/>
            <param argument="--no-chaining" type="boolean" truevalue="" falsevalue="--no-chaining" checked="true" label="Find best overall chain by chaining"/>
            <param argument="--out-min-prob" type="float" value="0.0005" min="0" max="1" label="Minimal probability in output (min-prob overrides if smaller)"/>
        </section>
    </inputs>

    <outputs>
        <expand macro="standard_outupt" />
        <data format="ps" name="ps_fileA" label="${tool.name} on ${on_string}: chain in RNA 1 (postscript)">
            <filter>'postscript' in outputs</filter>
        </data>
        <data format="ps" name="ps_fileB" label="${tool.name} on ${on_string}: chain in RNA 2 (postscript)">
            <filter>'postscript' in outputs</filter>
        </data>
        <data format="txt" name="anchors_fasta" label="${tool.name} on ${on_string}: anchor constraints from chain (fasta)">
            <filter>'anchors-fasta' in outputs</filter>
        </data>
        <data format="txt" name="anchors_ppA" label="${tool.name} on ${on_string}: anchors for RNA 1 (pp)">
            <filter>'anchors-pp' in outputs</filter>
        </data>
        <data format="txt" name="anchors_ppB" label="${tool.name} on ${on_string}: anchors for RNA 2 (pp)">
            <filter>'anchors-pp' in outputs</filter>
        </data>
        <data format="clustal" name="clustal" label="${tool.name} on ${on_string}: chain as alignment (clustal)">
            <filter>'clustal' in outputs</filter>
        </data>
        <data format="tabular" name="epm_list" label="${tool.name} on ${on_string}: list of epms">
            <filter>'epm_list' in outputs</filter>
        </data>
        <data format="tabular" name="chained_epm_list" label="${tool.name} on ${on_string}: list of epms in chain">
            <filter>'chained_epm_list' in outputs</filter>
        </data>
    </outputs>

    <tests>
        <test expect_num_outputs="2">
            <param name="inputA" value="tRNA_2-1.fa"/>
            <param name="inputB" value="tRNA_2-2.fa"/>
            <param name="outputs" value="epm_list"/>
            <output name="epm_list" file="tRNA_2.epms"/>
            <output name="stdout">
                <assert_contents>
                    <has_text text="LCSEPM preprocessing..."/>
                    <has_text text="#EPMs:"/>
                </assert_contents>
            </output>
        </test>
    </tests>

    <help><![CDATA[ **LocARNA -- Pairwise matching and folding of RNAs (ExpARNA-P)**

Pairwise matching and folding tool of the LocARNA suite (ExpARNA-P).

**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.b

**Output.**

The program enumerates exactly matching local substructures (exact
pattern matches = EPMs) and optionally chains them. It returns lists
of chained and unchained matches, visualizations of the results and
anchor constraints for alignment.


For more information, see
.. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
    ]]></help>

    <expand macro="citations" />

</tool>