Added rna_eps outpu to some tools. Changed labels of outputs to autom…

…atically generated.
bgruening · Feb 2, 2015 · ffd46e6 · ffd46e6
1 parent 0d56041
commit ffd46e6
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Showing 21 changed files with 92 additions and 90 deletions.
diff --git a/rna_tools/vienna_rna/rna2dfold.xml b/rna_tools/vienna_rna/rna2dfold.xml
@@ -75,7 +75,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="txt" name="out_file" label="${tool.name} on ${on_string}"/>
+        <data format="txt" name="out_file"/>
     </outputs>
     <tests>
     </tests>

diff --git a/rna_tools/vienna_rna/rnaaliduplex.xml b/rna_tools/vienna_rna/rnaaliduplex.xml
@@ -48,7 +48,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="txt" name="out_file" label="${tool.name} on ${on_string}"/>
+        <data format="txt" name="out_file"/>
     </outputs>
     <tests>
     </tests>

diff --git a/rna_tools/vienna_rna/rnaalifold.xml b/rna_tools/vienna_rna/rnaalifold.xml
@@ -89,8 +89,8 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="txt" name="tabularFile" label="Tabular File"/>
-        <data format="tar" name="imagesFile" label="Image File"/>
+        <data format="txt" name="tabularFile"/>
+        <data format="tar" name="imagesFile"/>
     </outputs>
     <tests>
     </tests>

diff --git a/rna_tools/vienna_rna/rnacofold.xml b/rna_tools/vienna_rna/rnacofold.xml
@@ -22,7 +22,6 @@
             $advancedOptions.noclosinggu
             $advancedOptions.notetra
         #end if
-        ; tar -cf $imagesFile *.ps
 ]]>
     </command>
     <inputs>
@@ -34,7 +33,7 @@
             <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
             <option value="3">3: allow coaxial stacking</option>
         </param>
-        <param name="pf" type="boolean" checked="false" truevalue="-p" falsevalue="" label="calculate partition function" help="-p"/>
+        <param name="pf" type="boolean" checked="false" truevalue="--partfunc" falsevalue="" label="Calculate Partition Function" help="--partfunc"/>
         <param name="allpf" type="boolean" checked="false" truevalue="--all_pf" falsevalue="" label="Calculate homo-dimers" help="--all_pf"/>
         <conditional name="advancedOptions">
             <param name="advancedSelector" type="select" label="advanced options">
@@ -53,8 +52,14 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="txt" name="tabularFile" label="Tabular File"/>
-        <data format="tar" name="imagesFile" label="Image File"/>
+        <data format="txt" name="tabularFile"/>
+        <data format="txt" name="structure">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)_ss\.ps" ext="eps" visible="true"/>
+        </data>
+        <data format="txt" name="dotplot">
+            <filter>pf is True</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
+        </data>
     </outputs>
     <tests>
     </tests>
@@ -78,8 +83,9 @@ Two different RNA sequences can be specified concatenated with the '&' character
 
 **Outputs**
 
-- energy of the RNA sequences and the dimers
-- several possible postscript images bundled together in a tar file
+- Energies of the RNA sequences and the dimers
+- Structure images
+- Dot Plot Matrix images (if --partfunc is used)
 
 
 @citation@

diff --git a/rna_tools/vienna_rna/rnadistance.xml b/rna_tools/vienna_rna/rnadistance.xml
@@ -43,7 +43,7 @@
         <param name="backtrack" type="boolean" checked="false" truevalue="--backtrack" falsevalue="" label="Print an alignment" help="--backtrack"/>
     </inputs>
     <outputs>
-        <data format="txt" name="outfile" label="RNADistance"/>
+        <data format="txt" name="outfile"/>
     </outputs>
     <tests>
     </tests>

diff --git a/rna_tools/vienna_rna/rnaduplex.xml b/rna_tools/vienna_rna/rnaduplex.xml
@@ -48,7 +48,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="txt" name="tabularFile" label="RNAduplex"/>
+        <data format="txt" name="tabularFile"/>
     </outputs>
     <tests>
     </tests>

diff --git a/rna_tools/vienna_rna/rnaeval.xml b/rna_tools/vienna_rna/rnaeval.xml
@@ -48,7 +48,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="txt" name="tabularFile" label="RNAeval"/>
+        <data format="txt" name="tabularFile"/>
     </outputs>
     <tests>
     </tests>

diff --git a/rna_tools/vienna_rna/rnafold.xml b/rna_tools/vienna_rna/rnafold.xml
@@ -7,73 +7,74 @@
         <token name="@EXECUTABLE@">RNAfold</token>
         <import>macros.xml</import>
     </macros>
-    <command interpreter="python">
-<![CDATA[
-        rnafold.py -i $fasta_input -o1 $tabularFile -o2 $imagesFile
-        #if $pfselect.pf=="yes"
-            --partitionFunction
-        #end if
-
-        #if $measelect.mea=="yes"
-            --mea $measelect.meavalue
-        #end if
-
-        --parameters " -T$temperature -d$dangling
-            #if $varExists('$advancedOptions.noconversion')
-                $advancedOptions.noconversion
-                $advancedOptions.gquad
-                $advancedOptions.nolp
-                $advancedOptions.nogu
-                $advancedOptions.noclosinggu
-                $advancedOptions.notetra
-                $advancedOptions.canonicalonly
-                $advancedOptions.circular
-            #end if
-        "
+    <command>
+ <![CDATA[
+    RNAfold
+    -T $temperature                                           
+    --dangles=$dangling
+    #if $measelect.mea == "yes":
+        --MEA=$measelect.meavalue
+    #else
+        $measelect.pf
+    #end if
+    #if $varExists('$advancedOptions.nogu'):
+        $advancedOptions.noconversion
+        $advancedOptions.gquad
+        $advancedOptions.nolp
+        $advancedOptions.nogu
+        $advancedOptions.noclosinggu
+        $advancedOptions.canonicalonly
+        $advancedOptions.circular
+    #end if
+
+    < $fasta_input
+    
+    > $tabular_file
 ]]>
     </command>
 
     <inputs>
     <param format="fasta" name="fasta_input" type="data" label="FASTA file"/>
-        <param name="temperature" size="6" type="float" value="37.0" label="temperature [°C]" help="-T"/>
+        <param name="temperature" size="6" type="float" value="37.0" label="Temperature [°C]" help="-T"/>
         <param name="dangling" type="select" label="how to treat dangling end energies" help="-d">
             <option value="0">0: ignore dangling ends</option>
             <option value="1">1: unpaired bases participate in one dangling end only</option>
             <option value="2" selected="True">2: unpaired bases participate in all dangling ends</option>
             <option value="3">3: allow coaxial stacking</option>
         </param>
-        <conditional name="pfselect">
-            <param name="pf" type="select" label="calculate partition function" help="--partfunc">
-                <option value="no">no</option>
-                <option value="yes">yes</option>
-            </param>
-        </conditional>
         <conditional name="measelect">
-            <param name="mea" type="select" label="calculate maximum expected accuracy" help="--MEA">
-                <option value="no">no</option>
-                <option value="yes">yes</option>
+            <param name="mea" type="select" label="Calculate Maximum Expected accuracy" help="--MEA">
+                <option value="no">No</option>
+                <option value="yes">Yes</option>
             </param>
             <when value="yes">
                 <param name="meavalue" size="6" type="float" value="1.0" label="Gamma Value"/>
             </when>
+            <when value="no">
+                <param name="pf" type="boolean" checked="false" truevalue="--partfunc" falsevalue="" label="Calculate Partition Function" help="--partfunc"/>
+            </when>
         </conditional>
         <conditional name="advancedOptions">
             <param name="advancedSelector" type="boolean" checked="false" label=" advanced options"/>
             <when value="true">
                 <param name="noconversion" type="boolean" truevalue="--noconv" falsevalue="" checked="false" label="no conversion" help="--noconv  do not convert thymine to uracile (T -> U)."/>
                 <param name="gquad" type="boolean" truevalue="--gquad" falsevalue="" checked="false" label="G Quadruplex formation" help="-g  take into account G Quadruplex formation"/>
                 <param name="nolp" type="boolean" truevalue="--noLP" falsevalue="" checked="false" label="No lonely pairs" help="--noLP  don't allow lonely pairs."/>
-                <param name="nogu" type="boolean" truevalue="--noGU" falsevalue="" checked="false" label="No GU pairing" help="--noGU  don't allow pairing of G and U."/>
-                <param name="noclosinggu" type="boolean" truevalue="--noClosingGU" falsevalue="" checked="false" label="No GU pairing at the ends" help="--noClosingGU  don't allow pairing of G and U at the ends of helices."/>
-                <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/>
+                <param name="nogu" type="boolean" truevalue="--noGU" falsevalue="" checked="false" label="No GU pairing" help="--noGU  don't allow pairing of G and U."/> <param name="noclosinggu" type="boolean" truevalue="--noClosingGU" falsevalue="" checked="false" label="No GU pairing at the ends" help="--noClosingGU  don't allow pairing of G and U at the ends of helices."/> <param name="notetra" type="boolean" truevalue="--noTetra" falsevalue="" checked="false" label="No stabilization for loops, hairpins etc." help="--noTetra"/>
                 <param name="canonicalonly" type="boolean" truevalue="--canonicalBPonly" falsevalue="" checked="false" label="Canonical basepairing only" help="--canonicalBPonly"/>
                 <param name="circular" type="boolean" truevalue="--circ" falsevalue="" checked="false" label="Assume circular RNA structure" help="--circ"/>
             </when>
         </conditional>
     </inputs>
     <outputs>
-        <data format="txt" name="tabularFile" label="Tabular File"/>
-        <data format="tar" name="imagesFile" label="Image File"/>
+        <data format="tabular" name="tabular_file"/>
+        <data format="txt" name="structure">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)_ss\.ps" ext="eps" visible="true"/>
+        </data>
+        <data format="txt" name="dotplot">
+            <filter>measelect['pf'] is True</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
+        </data>
     </outputs>
     <tests>
     </tests>
@@ -112,24 +113,11 @@ RNAfold requires one input file
 
 **Outputs**
 
-- Tab-seperated file
-    - 1st column: header line of FASTA input
-    - 2nd column: sequence
-    - 3rd column: dot-bracket notation
-    - 4th column: free energy
-    - if the partition function or the mean ensemble accuracy is calculated then more columns are added
-    - 5th column: dot-bracket notation
-    - 6th column: free energy
-    - 7th column: dot-bracket notation
-    - 8th column: free energy
-    - if the mean ensemble accuracy is calculated then even more columns are added
-    - 9th column: dot-bracket
-    - 10th column:free energy
-    - 9/11th column: frequency of mfe ensemble, ensemble diversity
+- Secondary structures in dot-bracket notation
 
 - several possible postscript images bundled together in a tar file
     - secondary structure for each sequence in the input file
-    - if partition function is calculated then also the pairing probabilty matrix is generated for each sequence
+    - if partition function is calculated (--MEA or --partfunc is set) then also the pairing probabilty matrix is generated for each sequence 
 
 
 @citation@

diff --git a/rna_tools/vienna_rna/rnaheat.xml b/rna_tools/vienna_rna/rnaheat.xml
@@ -49,7 +49,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="txt" name="output" label="RNAheat"/>
+        <data format="txt" name="output"/>
     </outputs>
     <tests>
     </tests>

diff --git a/rna_tools/vienna_rna/rnainverse.xml b/rna_tools/vienna_rna/rnainverse.xml
@@ -54,7 +54,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="txt" name="outfile" label="${tool.name} on ${on_string}"/>
+        <data format="txt" name="outfile"/>
     </outputs>
     <tests>
     </tests>

diff --git a/rna_tools/vienna_rna/rnalalifold.xml b/rna_tools/vienna_rna/rnalalifold.xml
@@ -63,7 +63,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="txt" name="output" label="RNALalifold"/>
+        <data format="txt" name="output" />
         <!-- the program does not seem to generate a dot plot, even though that is implied in the help -->
         <!--<data format="tar" name="imagesFile" label="RNALalifold images"/>-->
     </outputs>

diff --git a/rna_tools/vienna_rna/rnalfold.xml b/rna_tools/vienna_rna/rnalfold.xml
@@ -58,7 +58,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="txt" name="out_file" label="${tool.name} on ${on_string}"/>
+        <data format="txt" name="out_file"/>
     </outputs>
     <tests>
     </tests>

diff --git a/rna_tools/vienna_rna/rnapaln.xml b/rna_tools/vienna_rna/rnapaln.xml
@@ -30,7 +30,6 @@
         #if $backtrack and str($compare)=="m"
             ; cat backtrack.file >> $outfile
         #end if
-        ; tar -cf $imagesFile *.ps
 ]]>
     </command>
 
@@ -73,8 +72,10 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="txt" name="output" label="RNApaln"/>
-        <data format="tar" name="imagesFile" label="RNALpaln images"/>
+        <data format="txt" name="output"/>
+        <data format="txt" name="dotplot">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
+        </data>
     </outputs>
     <tests>
     </tests>

diff --git a/rna_tools/vienna_rna/rnapdist.xml b/rna_tools/vienna_rna/rnapdist.xml
@@ -27,7 +27,6 @@
             ; cat backtrack.file >> $outfile
         #end if
 
-        ; tar -cf $imagesFile *.ps
 ]]>
     </command>
 
@@ -62,8 +61,10 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="txt" name="output" label="RNApdist"/>
-        <data format="tar" name="imagesFile" label="RNApdist Images"/>
+        <data format="txt" name="output"/>
+        <data format="txt" name="dotplot">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
+        </data>
     </outputs>
     <tests>
     </tests>

diff --git a/rna_tools/vienna_rna/rnapkplex.xml b/rna_tools/vienna_rna/rnapkplex.xml
@@ -23,7 +23,6 @@
             $advancedOptions.noclosinggu
             $advancedOptions.notetra
         #end if
-        ; tar -cf $imagesFile *.ps
 ]]>
     </command>
 
@@ -49,8 +48,10 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="txt" name="output" label="RNAPKplex"/>
-        <data format="tar" name="imagesFile" label="RNAPKplex images"/>
+        <data format="txt" name="output"/>
+        <data format="txt" name="dotplot">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.ps" ext="eps" visible="true"/>
+        </data>
     </outputs>
     <tests>
     </tests>
@@ -80,7 +81,7 @@ The input format is similar to fasta except that even long sequences may not be
 **Outputs**
 
 - secondary structure in dot-bracket format
-- several possible postscript images bundled together in a tar file
+- Images of the calculated structures
 
 
 @citation@

diff --git a/rna_tools/vienna_rna/rnaplex.xml b/rna_tools/vienna_rna/rnaplex.xml
@@ -95,7 +95,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="txt" name="output" label="RNAplex"/>
+        <data format="txt" name="output"/>
     </outputs>
     <tests>
     </tests>

diff --git a/rna_tools/vienna_rna/rnaplfold.xml b/rna_tools/vienna_rna/rnaplfold.xml
@@ -28,7 +28,7 @@
             $advancedOptions.noclosinggu
             $advancedOptions.notetra
         #end if
-        ;ls *.ps *_basepairs *_lunp *_openen > files.tmp
+        ;ls *_basepairs *_lunp *_openen > files.tmp
         ;tar -cf $outputf --files-from=files.tmp
 
 ]]>
@@ -72,7 +72,10 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="tar" name="outputf" label="RNAplfold output"/>
+        <data format="txt" name="dotplot">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)_dp\.ps" ext="rna_eps" visible="true"/>
+        </data>
+        <data format="tar" name="outputf"/>
     </outputs>
     <tests>
     </tests>
@@ -96,7 +99,9 @@ RNAPplfold requires one input file
 
 **Outputs**
 
-For each structure in the Fasta input a postscript image with dot-plot of the pairing probabilities is generated. Different output is generated with the "--ulength", "--print_onthefly" and "--opening_energies" flags. The output is packed in a tar file.
+For each structure in the Fasta input a postscript image with dot-plot of the pairing probabilities is generated. Different output is generated with the "--ulength", "--print_onthefly" and "--opening_energies" flags.
+The Dot Plot Matrices are stored in a Postscript file.
+The other output is packed in a tar file.
 
 
 @citation@

diff --git a/rna_tools/vienna_rna/rnaplot.xml b/rna_tools/vienna_rna/rnaplot.xml
@@ -46,7 +46,7 @@
     </inputs>
 
     <outputs>
-        <data format="tar" name="imagesFile" label="RNAplot images"/>
+        <data format="tar" name="imagesFile"/>
     </outputs>
     <tests>
     </tests>