--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mlocarna.xml	Tue Dec 06 11:39:14 2016 -0500
@@ -0,0 +1,195 @@
+<tool id="mlocarna" name="LocARNA" version="@VERSION@.0">
+    <description>
+        Multiple Alignment and Folding of RNAs
+    </description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    
+    <expand macro="requirements" />
+
+    <expand macro="stdio" />
+    
+    <expand macro="version" />
+    
+    <command><![CDATA[
+    mlocarna
+    
+    '$input_data'
+    #if 'stockholm' in str($outputs).split(","):
+    --stockholm
+    #end if
+
+    --tgtdir 'outdir'
+    
+    ## -------------------- alignment mode and specific options
+
+    #if str($alignment_mode.alignment_mode_selector) == "global_locarna"
+        $alignment_mode.free_endgaps
+    #else if str($alignment_mode.alignment_mode_selector) == "local_locarna"
+        --sequ-local on
+    #else if str($alignment_mode.alignment_mode_selector) == "probabilistic"
+        --probabilistic
+        $alignment_mode.consistency_transformation
+        
+        #if str($alignment_mode.iterate) == "true"
+            --iterate
+            --iterations $alignment_mode.iterations
+        #end if
+    #else if str($alignment_mode.alignment_mode_selector) == "sparse"
+        --sparse
+    #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 $Folding.plfold_span>=0
+        --plfold-span $Folding.plfold_span
+        --plfold-winsize $Folding.plfold_winsize
+    #end if
+    
+    --rnafold-temperature $Folding.rnafold_temperature
+    
+    ## -------------------- 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
+    --max-bps-length-ratio $Heuristics.max_bps_length_ratio
+    
+    $Heuristics.alifold_consensus_dp
+
+    ## -------------------- other parameters
+    
+    $Other.lonely_pairs
+
+    $stdout_verbosity
+
+    #if str($stdout_verbosity) != "--quiet":
+        > '$stdout'
+    #end if
+    ]]></command>
+
+    <inputs>
+        <param name="input_data" type="data" format="text,fasta" label="Sequence input"
+               help="Sequence input in fasta format, optionally with locarna-specific extensions"
+               />
+        
+        <conditional name="alignment_mode">
+            <param name="alignment_mode_selector" type="select" label="Alignment mode">
+                <option value="global_locarna">Global alignment (LocARNA)</option>
+                <option value="local_locarna">Local alignment (LocARNA)</option>
+                <option value="probabilistic">Probabilistic alignment (LocARNA-P)</option>
+                <option value="sparse">Global alignment (SPARSE)</option>
+            </param>
+            <when value="global_locarna">
+                <param name="free_endgaps" type="select" label="Free endgaps">
+                    <option value="">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>
+            </when>
+            <when value="local_locarna" />
+            <when value="probabilistic">
+                <param name="consistency_transformation" type="boolean" 
+                       truevalue="--consistency-transformation" falsevalue="" 
+                       checked="true" label="Consistency transformation" 
+                       help="--consistency-transformation" />
+                <param name="iterate" type="boolean"
+                       truevalue="true" falsevalue="false"
+                       checked="false" label="Iterative refinement"
+                       help="--iterate" />
+                <param name="iterations" type="integer"
+                       value="1" label="Number of refinement iterations"
+                       help="--iterations num" />
+            </when>
+            <when value="sparse" />
+        </conditional>
+        
+        <param name="outputs" type="select" display="checkboxes" multiple="True" 
+               label="Output options">
+            <option value="clustal" selected="True">Output alignment
+            in Clustalw format</option>
+            <option value="stockholm" selected="False">Output
+            alignment in Stockholm 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>
+            <option value="--moreverbose">More 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" />
+        </section>
+
+        <section name="Heuristics" title="Heuristic parameters">
+            <expand macro="common_heuristic_parameters" />
+        </section>
+
+        <section name="Other" title="Other parameters">
+            <expand macro="common_other_parameters" />
+            <param name="lonely_pairs" type="boolean" truevalue="--LP" falsevalue="--noLP" 
+                   checked="false" label="Allow lonely base-pairs" help="(--LP/--noLP)" />
+        </section>
+    </inputs>
+    
+    <outputs>
+        <expand macro="common_outputs" />
+    </outputs>
+    
+    <tests>
+        <test>
+            <param name="input_data" value="archaea.fa" />
+            <param name="stdout_verbosity" value="" />
+            <output name="stdout" file="archaea-default.stdout" />
+        </test>
+        <test>
+            <param name="input_data" value="haca.snoRNA.fa" />
+            <param name="stdout_verbosity" value="" />
+            <output name="stdout" file="haca.snoRNA-default.stdout" />
+        </test>
+        <test>
+            <param name="input_data" value="archaea.fa" />
+            <param name="stdout_verbosity" value="" />
+            <param name="outputs" value="clustal" />
+            <param name="alignment_mode_selector" value="probabilistic" />
+            <output name="clustal" file="archaea-probabilistic.aln" />
+        </test>
+    </tests>
+
+    <help><![CDATA[ **Multiple alignment of RNAs**
+    
+For more information, see     
+.. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
+    ]]></help>
+
+    <expand macro="citations" />
+    
+</tool>