--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/locarna_reliability_profile.xml	Wed Dec 28 18:52:45 2016 -0500
@@ -0,0 +1,196 @@
+<tool id="locarna_reliability_profile" name="LocARNA reliability-profile" version="@VERSION@.0">
+    <description>
+        Plot reliability profile for probabilistic mlocarna
+    </description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    
+    <expand macro="requirements" />
+
+    <expand macro="stdio" />
+    
+    <expand macro="version" />
+    
+    <command><![CDATA[
+    (if file '$input_archive' | grep 'gzip compressed' > /dev/null ;
+    then tar xzf '$input_archive' ;
+    else tar xf '$input_archive' ;
+    fi)
+    &&
+    reliability-profile.pl mlocarna_results
+
+    --output-format='$output_format'
+
+    #if $output_format == 'pdf'
+         --out '$pdf_output_plot'
+    #else if $output_format == 'png'
+         --out '$png_output_plot'
+    #end if
+
+    #if str($title) != ""
+        --title '$title'
+    #end if
+
+    #if str($seqname) != ""
+        --seqname $seqname
+    #end if
+
+    --beta $beta
+    --structure-weight $structure_weight
+    
+    #if str($signals)!=""
+        --signals '$signals'
+    #end if
+
+    --offset $offset
+
+    #if $write_rscript:
+        --write-R-script '$rscript_output'
+    #end if
+
+    #if $write_subsequence
+        --write-subseq
+    #end if
+    
+    $predict
+    $fit_once_on
+    $show_sw
+    $rev_compl
+
+    > '$stdout'
+    ]]></command>
+    
+    <inputs>
+        <param name="input_archive" type="data" format="tar.gz" label="MLocARNA archive"
+               help="Archive of MLocARNA results (tar or tar.gz as generated by running
+                     mlocarna in probabilistic alignment mode)." />
+
+        <param name="title" type="text" label="Plot title"
+               help="Title of the plot"
+               />
+
+        <param name="seqname" type="text" label="Reference sequence"
+               help="Project to a reference sequence. Provide one of the sequence names in the alignment input
+                     or leave blank to plot without projection."
+               />
+
+        <param name="predict" type="boolean" checked="True"
+               truevalue="" falsevalue="--dont-predict"
+               argument="dont-predict"
+               help="Turn on/off predicting."
+               />
+
+        <param name="fit_once_on" type="boolean" checked="False"
+               truevalue="--fit-once-on" falsevalue=""
+               argument="fit-once-on"
+               help="Predict exactly one 'on'-region"
+               />
+
+        <param name="show_sw" type="boolean" checked="True"
+               truevalue="--show-sw" falsevalue=""
+               argument="show-sw"
+               help="Show the influence of structure weight."
+               />
+
+        <param name="rev_compl" type="boolean" checked="False"
+               truevalue="--revcompl" falsevalue=""
+               argument="revcompl"
+               help="Plot and fit a reverse complement."
+               />
+
+        <param argument="beta" help="Inverse temperature for fitting." 
+               type="float" value="12.0" min="1.0" max="25.0" />
+        
+        <param name="structure_weight" argument="structure-weight"
+               type="float" value="1.0" min="0.0" max="8.0"
+               help="Weight of structure against sequence (1.0 means equal)"
+               />
+ 
+        <param argument="offset" help="Genomic offset." 
+               type="integer" value="1" />
+        
+        <param name="signals" type="text" label="List of signals"
+               help="List of '{from to} orientation' signal specifications. Show signals in plot
+                     and compared infered signal to them. Ranges 'from to' can be repeated; 
+                     the orientation must be either +1 or -1.
+                     The specifications of the single signals are separated by ';'. Example of two signal, 
+                     where the first one consists of two ranges: 1 15 20 30 +1; 15 45 -1"
+               >
+            <sanitizer invalid_char=" ">
+                <valid initial="string.digits"> <add value="+" /> <add value="-" /> <add value=";" /> </valid>
+            </sanitizer>
+        </param>
+       
+        <param name="output_format" type="select" 
+               label="Output options">
+            <option value="pdf" selected="True">Plot in pdf
+            format</option>
+            <option value="png" selected="False">Plot in png format</option>
+        </param>
+
+        <param name="write_rscript" type="boolean" argument="write-R-script"
+               label="Write R script" checked="False"
+               help="Write R script that can produce the output plot."
+               />
+
+        <param name="write_subsequence" type="boolean" argument="write-subseq"
+               label="Write Subsequence" checked="False"
+               help="Write subsequence in output."
+               />
+        
+    </inputs>
+               
+    
+    <outputs>
+        <data format="pdf" name="pdf_output_plot"
+              label="${tool.name} reliability plot (pdf) ${on_string}">
+            <filter>output_format == 'pdf'</filter>
+        </data>
+        <data format="png" name="png_output_plot"
+              label="${tool.name} reliability plot (png) ${on_string}">
+            <filter>output_format == 'png'</filter>
+        </data>
+        <data format="txt" name="rscript_output"
+              label="${tool.name} reliability plot (R script) ${on_string}">
+            <filter> write_rscript is True </filter>
+        </data>
+        <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}" />
+    </outputs>
+    
+    <tests>
+        <test>
+            <param name="input_archive" value="archaea.tar.gz" />
+            <param name="write_rscript" value="True" />
+            <output name="rscript_output" file="archaea_relplot.scr" lines_diff="2" />
+        </test>
+    </tests>
+
+    <help><![CDATA[**Reliability Profiles for Multiple RNA
+Alignment**
+    
+This tool draws reliability profiles for mlocarna alignments that have
+been computed in probabilistic alignment mode. Moreover, it predicts
+reliably aligned regions, which can be used to determine the
+boundaries of well conserved structured RNA motifs in less closely
+related sequence context.
+    
+**Input.**
+Results archive of an alignment by the mlocarna tool; for this
+purpose, mlocarna must be run in probabilistic mode in order to
+generate the required reliability information.
+
+**Output.**
+Plot of the reliability profile for the input alignment. Moreover,
+a signal prediction is performed and predicted regions are
+annotated in the plot.
+
+
+For more information, see
+.. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
+    ]]></help>
+
+    <expand macro="citations" />
+    
+</tool>