--- a/locarna_reliability_profile.xml	Mon Dec 05 14:29:00 2022 +0000
+++ b/locarna_reliability_profile.xml	Mon Aug 19 18:52:31 2024 +0000
@@ -6,11 +6,8 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    
     <expand macro="requirements" />
-
     <expand macro="stdio" />
-    
     <expand macro="version" />
     
     <command><![CDATA[
@@ -63,93 +60,40 @@
     ]]></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 argument="--dont-predict" name="predict" type="boolean" checked="true"
-               truevalue="" falsevalue="--dont-predict"
-               help="Turn on/off predicting."
-               />
-
-        <param argument="--fit-once-on" type="boolean" checked="false"
-               truevalue="--fit-once-on" falsevalue=""
-               help="Predict exactly one 'on'-region"
-               />
-
-        <param argument="--show-sw" type="boolean" checked="true"
-               truevalue="--show-sw" falsevalue=""
-               help="Show the influence of structure weight."
-               />
-
-        <param argument="--revcompl" name="rev_compl" type="boolean" checked="false"
-               truevalue="--revcompl" falsevalue=""
-               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 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 argument="--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"
-               >
+        <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 argument="--dont-predict" name="predict" type="boolean" checked="true" truevalue="" falsevalue="--dont-predict" help="Turn on/off predicting."/>
+        <param argument="--fit-once-on" type="boolean" checked="false" truevalue="--fit-once-on" falsevalue="" help="Predict exactly one 'on'-region"/>
+        <param argument="--show-sw" type="boolean" checked="true" truevalue="--show-sw" falsevalue="" help="Show the influence of structure weight."/>
+        <param argument="--revcompl" name="rev_compl" type="boolean" checked="false" truevalue="--revcompl" falsevalue="" 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 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 argument="--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>
+        <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."
-               />
-        
+        <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} on ${on_string}: plot">
+        <data format="pdf" name="pdf_output_plot" label="${tool.name} on ${on_string}: PDF plot">
             <filter>output_format == 'pdf'</filter>
         </data>
-        <data format="png" name="png_output_plot"
-              label="${tool.name} on ${on_string}: plot">
+        <data format="png" name="png_output_plot" label="${tool.name} on ${on_string}: PNG plot">
             <filter>output_format == 'png'</filter>
         </data>
-        <data format="txt" name="rscript_output"
-              label="${tool.name} on ${on_string}: R script ">
+        <data format="txt" name="rscript_output" label="${tool.name} on ${on_string}: R script ">
             <filter> write_rscript is True </filter>
         </data>
         <data format="txt" name="stdout" label="${tool.name} on ${on_string}: stdout" />
@@ -201,4 +145,4 @@
 
     <expand macro="citations" />
     
-</tool>
+</tool>
\ No newline at end of file