--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/locarna_pairwise_p.xml	Fri Jan 13 16:48:31 2017 -0500
@@ -0,0 +1,212 @@
+<tool id="locarna_pairwise_p" name="LocARNA Pairwise Probability Aligner" version="@VERSION@.0">
+    <description>
+        Partition Function and Probabilities from Pairwise Simultaneous Alignment and Folding of RNAs (LocARNA-P)
+    </description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    
+    <expand macro="requirements" />
+
+    <expand macro="stdio" />
+    
+    <expand macro="version" />
+   
+    <command><![CDATA[
+    locarna_p
+    
+    '$inputA'
+    '$inputB'
+    
+    --width 60
+    
+    @SCORING_ARGS@
+    
+    @FOLDING_ARGS@
+
+    @HEURISTIC_ARGS@
+    #if float($Heuristics.pf_scale) != 1.0
+       --pf-scale $Heuristics.pf_scale
+    #end if
+
+    ## -------------------- other parameters
+        
+    #if $Constraints.maxBPspan != -1
+        --maxBPspan $Constraints.maxBPspan
+    #end if
+
+    $Constraints.ignore_constraints
+
+    ## -------------------- probability parameters
+    $Probabilities.include_am_in_bm
+    #if float($Probabilities.min_bm_prob) != 0.0005
+       --min-bm-prob $Probabilities.min_bm_prob
+    #end if
+    #if float($Probabilities.min_am_prob) != 0.0005
+       --min-am-prob $Probabilities.min_am_prob
+    #end if
+
+    ## -------------------- output
+
+    #if not $arc_match_probs is None
+        --write-arcmatch-probs=$arc_match_probs
+    #end if
+    
+    #if not $base_match_probs is None
+        --write-basematch-probs=$base_match_probs
+    #end if
+    
+    @STDOUT_ARGS@
+
+    ]]></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="base_match_probs" selected="True">
+            Output base match probabilities</option>
+            <option value="arc_match_probs" selected="True">
+            Output arc match probabilities</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="Probabilities" title="Probability parameters">
+            <param name="include_am_in_bm" argument="include-am-in-bm"
+                   type="boolean"
+                   truevalue="--include-am-in-bm" falsevalue=""
+                   label="Include arc match cases in computation of base match probabilities" />
+            <param name="min_bm_prob" argument="min-bm-prob" 
+                   type="float"
+                   value="0.0005" min="0.0" max="1.0"
+                   label="Minimal base match probability"
+                   />
+            <param name="min_am_prob" argument="min-am-prob" 
+                   type="float"
+                   value="0.0005" min="0.0" max="1.0"
+                   label="Minimal arc match probability"
+                   />                  
+        </section>
+
+        <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" />
+            <expand macro="max_diff_parameters_aln" />
+            <param name="pf_scale" argument="pf-scale"
+                   type="float" value="1.0"
+                   label="Scaling of the partition function."
+                   help="Use (only) if standard scaling overflows." />
+        </section>
+
+        <section name="Constraints" title="Constraint parameters">
+            <expand macro="common_constraint_parameters" />
+        </section>
+
+    </inputs>
+    
+    <outputs>
+        <expand macro="standard_outupt" />
+        <data format="table" name="base_match_probs" label="${tool.name} base match probabilties on ${on_string}">
+            <filter>'base_match_probs' in outputs</filter>
+        </data>
+        <data format="table" name="arc_match_probs" label="${tool.name} arc match probabilties on ${on_string}">
+            <filter>'arc_match_probs' 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="arc_match_probs,base_match_probs"/>
+            <param name="min_bm_prob" value="0.01" />
+            <param name="min_am_prob" value="0.01" />
+            <output name="base_match_probs" file="tRNA_2.bmprobs" />
+            <output name="arc_match_probs" file="tRNA_2.amprobs" />
+        </test>
+    </tests>
+
+    <help><![CDATA[ **LocARNA -- Pairwise probability alignment of RNAs**
+
+Pairwise probability alignment tool of the LocARNA suite. This tool
+computes base and arc match probabilities from simultaneous RNA
+folding and alignment. It 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 tool writes two tables of base match and arc match probabilities, respectively. Rows
+in the base match probabilities table consist of
+
+  i j p
+
+where p is the probability of matching position i in the first sequence to position j in the second sequence. 
+
+For arc matchs, the table contains rows
+
+  i j k l p
+
+where p is the probability of matching the base pair (i,j) of sequence one to (k,l) of sequence two.
+
+Moreover, the partition function and further information can be written to standard out.
+
+For more information, see     
+.. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
+    ]]></help>
+
+    <expand macro="citations" />
+    
+</tool>