--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/locarna_exparnap.xml	Fri Jan 13 16:49:16 2017 -0500
@@ -0,0 +1,274 @@
+<tool id="locarna_exparnap" name="LocARNA Exact Matcher" version="@VERSION@.0">
+    <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@
+    --prob_unpaired_in_loop_threshold $Heuristics.prob_unpaired_in_loop_threshold
+    --prob_basepair_in_loop_threshold $Heuristics.prob_basepair_in_loop_threshold
+
+    @CONSTRAINT_ARGS@
+
+    ## -------------------- other parameters
+    #
+    #if str($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 name="no_stacking" 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 name="struct_mismatch_score" 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 name="diff_to_opt_score" argument="diff-to-opt-score"
+                           type="integer" value="-1" min="-20" max="0"
+                           label="Maximum score difference to optimum" />
+                    <param name="number_of_EPMs" argument="number-of-EPMs"
+                           type="integer" value="100" min="1" max="10000"
+                           label="Maximal number of EPMs" />
+                </when>
+            </conditional>
+
+            <param name="min_score" argument="min-score"
+                   type="integer" value="30" min="0" max="1000"
+                   label="Minimum score of EPM" />
+
+            <param name="inexact_struct_match" argument="inexact-struct-match" type="boolean"
+                   truevalue="--inexact-struct-match" falsevalue=""
+                   label="Allow inexact structure matches"/>
+
+            <param name="add_filter" 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 name="no_chaining" argument="no-chaining" type="boolean"
+                   truevalue="" falsevalue="--no-chaining" checked="True"
+                   label="Find best overall chain by chaining"/>
+
+            <param name="out_min_prob" 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} chain in RNA 1 (postscript) on ${on_string}">
+            <filter>'postscript' in outputs</filter>
+        </data>
+        <data format="ps" name="ps_fileB"
+              label="${tool.name} chain in RNA 2 (postscript) on ${on_string}">
+            <filter>'postscript' in outputs</filter>
+        </data>
+        <data format="txt" name="anchors_fasta"
+              label="${tool.name} anchor constraints from chain (fasta) on ${on_string}">
+            <filter>'anchors-fasta' in outputs</filter>
+        </data>
+        <data format="txt" name="anchors_ppA"
+              label="${tool.name} anchors for RNA 1 (pp) on ${on_string}">
+            <filter>'anchors-pp' in outputs</filter>
+        </data>
+        <data format="txt" name="anchors_ppB"
+              label="${tool.name} anchors for RNA 2 (pp) on ${on_string}">
+            <filter>'anchors-pp' in outputs</filter>
+        </data>
+        <data format="clustal" name="clustal"
+              label="${tool.name} chain as alignment (clustal) on ${on_string}">
+            <filter>'clustal' in outputs</filter>
+        </data>
+        <data format="tabular" name="epm_list"
+              label="${tool.name} list of epms on ${on_string}">
+            <filter>'epm_list' in outputs</filter>
+        </data>
+        <data format="tabular" name="chained_epm_list"
+              label="${tool.name} list of epms in chain on ${on_string}">
+            <filter>'chained_epm_list' 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="epm_list" />
+            <output name="epm_list" file="tRNA_2.epms" />
+        </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>