changeset 5:01ca3429ae6c draft

Uploaded

--- a/antarna.xml	Fri May 08 11:37:52 2015 -0400
+++ b/antarna.xml	Tue May 12 08:04:20 2015 -0400
@@ -107,8 +107,8 @@
 #if $Cseqw and $Cseqw is not None:
 -Cseqw $Cseqw
 #end if
+$ov
 $v
-$ov
 > $default]]></command>
   <inputs>
     <param label="Structure constraint using RNA dotbracket notation with fuzzy block constraint.  (-Cstr)" name="Cstr" type="text"/>
@@ -141,40 +141,28 @@
     <param checked="false" label="Prints additional output to the headers of the produced sequences. (-ov)" name="ov" type="boolean" truevalue="-ov" falsevalue=""/>
   </inputs>
   <outputs>
-    <data format="fasta" name="default"/>
+    <data format="fasta" hidden="false" name="default"/>
   </outputs>
-  <tests>
-    <test>
-      <param name="Cstr" value="..((..)).."/>
-      <param name="tGC" value="0.5"/>
-      <param name="n" value="2"/>
-      <output name="default">
-        <assert_contents>
-          <has_line_matching expression="[AGCT]{10}"/>
-        </assert_contents>
-      </output>
-    </test>
-  </tests>
   <help><![CDATA[   
+.
 
 ===========================
 antaRNA - ant assembled RNA                                   
 ===========================
   
-	- For antaRNA only the VIENNNA RNA Package must be installed on your linux system.
-	  antaRNA will only check, if the executables of RNAfold and RNAdistance of the ViennaRNA package can be found. If those programs are 
-	  not installed correctly, no output will be generated, an also no warning will be prompted.
-	  So the binary path of the Vienna Tools must be set up correctly in your system's PATH variable in order to run antaRNA correctly!
-    
-    - For questions and remarks please feel free to contact us at http://www.bioinf.uni-freiburg.de/
+- antaRNA uses the VIENNNA RNA Package
+    - specifically it uses RNAfold and RNAdistance to calculate energies of and distances between secondary structures (version 2.1.x)
+    - for the parametrization of antaRNA the version 2.1.3 of the ViennaRNA package was used 
 
-	Example calls:
-		antaRNA --Cstr "...(((...)))..." --tGC 0.5 -n 2
-		antaRNA --Cstr ".........AAA(((...)))AAA........." --tGC 0.5 -n 10 --output_file /path/to/antaRNA_TESTRUN -ov
-		antaRNA --Cstr "BBBBB....AAA(((...)))AAA....BBBBB" --Cseq "NNNNANNNNNCNNNNNNNNNNNGNNNNNNUNNN" --tGC 0.5 -n 10
+   
+- For questions and remarks please feel free to contact us at http://www.bioinf.uni-freiburg.de/
+
+Example calls:
+	antaRNA --Cstr "...(((...)))..." --tGC 0.5 -n 2
+	antaRNA --Cstr ".........AAA(((...)))AAA........." --tGC 0.5 -n 10 --output_file /path/to/antaRNA_TESTRUN -ov
+	antaRNA --Cstr "BBBBB....AAA(((...)))AAA....BBBBB" --Cseq "NNNNANNNNNCNNNNNNNNNNNGNNNNNNUNNN" --tGC 0.5 -n 10
+
 
 		]]></help>
-<citations>
-</citations>
 </tool>