# HG changeset patch
# User rnateam
# Date 1430398969 14400
# Node ID e2b8432942900183a753d3b0d1cea2e56a991d6b
# Parent  3abbf92e2ed2bb821b1e464760b1d93c4baf8e25
Uploaded

diff -r 3abbf92e2ed2 -r e2b843294290 antaRNA.xml
--- a/antaRNA.xml	Thu Apr 30 08:27:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,166 +0,0 @@
-<tool id="antaRNA.py" name="antaRNA.py" version="1.0">
-  <description>
-	Ant Colony Optimized RNA Sequence Design
-  </description>
-  <requirements>
-    <requirement type="package" version"2.2.12">pkiss</requirement>
-    <requirement type="package" version"3.2.5">rnashapes</requirement>
-    <requirement type="package" version"1.9">numpy</requirement>
-  </requirements>
-  <stdio>
-    <exit_code level="fatal" range="1:"/>
-  </stdio>
-  <version_command>python antaRNA.py --version</version_command>
-  <command interpreter="python"><![CDATA[antaRNA.py 
-#if $Cstr and $Cstr is not None:
--Cstr "$Cstr"
-#end if
-
-#if $tGC and $tGC is not None:
--tGC $tGC
-#end if
-
-#if $n and $n is not None:
--n $n
-#end if
-$GU
-
-#if $s and $s is not None:
--s $s
-#end if
-
-#if $ip and $ip is not None:
--ip $ip
-#end if
-
-#if $r and $r is not None:
--r $r
-#end if
-
-#if $CC and $CC is not None:
--CC $CC
-#end if
-
-#if $aTC and $aTC is not None:
--aTC $aTC
-#end if
-$p
-$pkPar
-
-#if $strategy and $strategy is not None:
---strategy $strategy
-#end if
-
-#if $tGCmax and $tGCmax is not None:
--tGCmax $tGCmax
-#end if
-
-#if $tGCvar and $tGCvar is not None:
--tGCvar $tGCvar
-#end if
-
-#if $t and $t is not None:
--t $t
-#end if
-
-#if $P and $P is not None:
--P $P
-#end if
-
-#if $of and $of is not None:
--of $of
-#end if
-
-#if $Cseq and $Cseq is not None:
--Cseq $Cseq
-#end if
-
-#if $l and $l is not None:
--l $l
-#end if
-
-#if $name and $name is not None:
---name $name
-#end if
-
-#if $a and $a is not None:
--a $a
-#end if
-
-#if $b and $b is not None:
--b $b
-#end if
-
-#if $er and $er is not None:
--er $er
-#end if
-
-#if $Cstrw and $Cstrw is not None:
--Cstrw $Cstrw
-#end if
-
-#if $Cgcw and $Cgcw is not None:
--Cgcw $Cgcw
-#end if
-
-#if $Cseqw and $Cseqw is not None:
--Cseqw $Cseqw
-#end if
-$v
-$ov
-> $default]]></command>
-  <inputs>
-    <param label="Structure constraint using RNA dotbracket notation with fuzzy block constraint.  (-Cstr)" name="Cstr" type="text"/>
-    <param label="Objective target GC content in [0,1]. (-tGC)" name="tGC" type="float" value="0"/>
-    <param label="Number of sequences which shall be produced.  (-n)" name="n" type="integer" value="0"/>
-    <param checked="false" label="Allowing GU base pairs.  (-GU)" name="GU" type="boolean" truevalue="-GU" falsevalue=""/>
-    <param default="none" label="Provides a seed value for the used pseudo random number generator. (-s)" name="s" type="text"/>
-    <param default="s" label="Select the improving method.  h=hierarchical, s=score_based. (-ip)" name="ip" type="text"/>
-    <param label="Amount of maximal terrain resets, until the best solution is retuned as solution. (-r)" name="r" type="integer" value="5"/>
-    <param label="Delimits the convergence count criterion for a reset. (-CC)" name="CC" type="integer" value="130"/>
-    <param label="Delimits the amount of internal ants for termination convergence criterion for a reset. (-aTC)" name="aTC" type="integer" value="50"/>
-    <param checked="false" label="Switch to pseudoknot based prediction using pKiss. Check the pseudoknot parameter usage!!! (-p)" name="p" type="boolean" truevalue="-p" falsevalue=""/>
-    <param checked="false" label="Enable optimized parameters for the usage of pseudo knots (Further parameter input ignored). (-pkPar)" name="pkPar" type="boolean" truevalue="-pkPar" falsevalue=""/>
-    <param default="A" label="Defining the pKiss folding strategy. (--strategy)" name="strategy" type="text"/>
-    <param label="Provides a maximum tGC value [0,1] for the case of uniform distribution sampling. The regular tGC value serves as minimum value. (-tGCmax)" name="tGCmax" type="float" value="-1.0"/>
-    <param label="Provides a tGC variance (sigma square) for the case of normal distribution sampling. The regular tGC value serves as expectation value (mu). (-tGCvar)" name="tGCvar" type="float" value="-1.0"/>
-    <param label="Provides a temperature for the folding algorithms. (-t)" name="t" type="float" value="37.0"/>
-    <param default="" label="Changes the energy parameterfile of RNAfold. If using this explicitly, please provide a suitable energy file delivered by RNAfold.  (-P)" name="P" type="text"/>
-    <param default="STDOUT" label="Provide a path and an output file, e.g. &quot;/path/to/the/target_file&quot;.  (-of)" name="of" type="text"/>
-    <param default="" label="Sequence constraint using RNA nucleotide alphabet {A,C,G,U} and wild-card &quot;N&quot;.  (-Cseq)" name="Cseq" type="text"/>
-    <param label="Sets the level of allowed influence of sequence constraint on the structure constraint [0:no influence; 3:extensive influence]. (-l)" name="l" type="integer" value="1"/>
-    <param default="antaRNA_" label="Defines a name which is used in the sequence output.  (--name)" name="name" type="text"/>
-    <param label="Sets alpha, probability weight for terrain path influence. [0,1] (-a)" name="a" type="float" value="1.0"/>
-    <param label="Sets beta, probability weight for terrain pheromone influence. [0,1]  (-b)" name="b" type="float" value="1.0"/>
-    <param label="Pheromone evaporation rate.  (-er)" name="er" type="float" value="0.2"/>
-    <param label="Structure constraint quality weighting factor. [0,1] (-Cstrw)" name="Cstrw" type="float" value="0.5"/>
-    <param label="GC content constraint quality weighting factor. [0,1] (-Cgcw)" name="Cgcw" type="float" value="5.0"/>
-    <param label="Sequence constraint quality weighting factor. [0,1] (-Cseqw)" name="Cseqw" type="float" value="1.0"/>
-    <param checked="false" label="Displayes intermediate output. (-v)" name="v" type="boolean" truevalue="-v" falsevalue=""/>
-    <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="txt" hidden="false" name="default"/>
-  </outputs>
-  <help><![CDATA[   
-.
-
-===========================
-antaRNA - ant assembled RNA                                   
-===========================
-  
-- 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 
-
-   
-- For questions and remarks please feel free to contact us at http://www.bioinf.uni-freiburg.de/
-
-Example calls:
-
-- python antaRNA.py --Cstr "...(((...)))..." --tGC 0.5 -n 2
-- python antaRNA.py --Cstr ".........AAA(((...)))AAA........." --tGC 0.5 -n 10 --output_file /path/to/antaRNA_TESTRUN -ov
-- python antaRNA.py --Cstr "BBBBB....AAA(((...)))AAA....BBBBB" --Cseq "NNNNANNNNNCNNNNNNNNNNNGNNNNNNUNNN" --tGC 0.5 -n 10
-	]]></help>
-</tool>
-
diff -r 3abbf92e2ed2 -r e2b843294290 antarna.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/antarna.xml	Thu Apr 30 09:02:49 2015 -0400
@@ -0,0 +1,166 @@
+<tool id="antarna" name="antaRNA" version="1.1">
+  <description>
+	Ant Colony Optimized RNA Sequence Design
+  </description>
+  <requirements>
+    <requirement type="package" version"2.2.12">pkiss</requirement>
+    <requirement type="package" version"3.2.5">rnashapes</requirement>
+    <requirement type="package" version"1.9">numpy</requirement>
+  </requirements>
+  <stdio>
+    <exit_code level="fatal" range="1:"/>
+  </stdio>
+  <version_command>python antaRNA.py --version</version_command>
+  <command interpreter="python"><![CDATA[antaRNA.py 
+#if $Cstr and $Cstr is not None:
+-Cstr "$Cstr"
+#end if
+
+#if $tGC and $tGC is not None:
+-tGC $tGC
+#end if
+
+#if $n and $n is not None:
+-n $n
+#end if
+$GU
+
+#if $s and $s is not None:
+-s $s
+#end if
+
+#if $ip and $ip is not None:
+-ip $ip
+#end if
+
+#if $r and $r is not None:
+-r $r
+#end if
+
+#if $CC and $CC is not None:
+-CC $CC
+#end if
+
+#if $aTC and $aTC is not None:
+-aTC $aTC
+#end if
+$p
+$pkPar
+
+#if $strategy and $strategy is not None:
+--strategy $strategy
+#end if
+
+#if $tGCmax and $tGCmax is not None:
+-tGCmax $tGCmax
+#end if
+
+#if $tGCvar and $tGCvar is not None:
+-tGCvar $tGCvar
+#end if
+
+#if $t and $t is not None:
+-t $t
+#end if
+
+#if $P and $P is not None:
+-P $P
+#end if
+
+#if $of and $of is not None:
+-of $of
+#end if
+
+#if $Cseq and $Cseq is not None:
+-Cseq $Cseq
+#end if
+
+#if $l and $l is not None:
+-l $l
+#end if
+
+#if $name and $name is not None:
+--name $name
+#end if
+
+#if $a and $a is not None:
+-a $a
+#end if
+
+#if $b and $b is not None:
+-b $b
+#end if
+
+#if $er and $er is not None:
+-er $er
+#end if
+
+#if $Cstrw and $Cstrw is not None:
+-Cstrw $Cstrw
+#end if
+
+#if $Cgcw and $Cgcw is not None:
+-Cgcw $Cgcw
+#end if
+
+#if $Cseqw and $Cseqw is not None:
+-Cseqw $Cseqw
+#end if
+$v
+$ov
+> $default]]></command>
+  <inputs>
+    <param label="Structure constraint using RNA dotbracket notation with fuzzy block constraint.  (-Cstr)" name="Cstr" type="text"/>
+    <param label="Objective target GC content in [0,1]. (-tGC)" name="tGC" type="float" value="0"/>
+    <param label="Number of sequences which shall be produced.  (-n)" name="n" type="integer" value="0"/>
+    <param checked="false" label="Allowing GU base pairs.  (-GU)" name="GU" type="boolean" truevalue="-GU" falsevalue=""/>
+    <param default="none" label="Provides a seed value for the used pseudo random number generator. (-s)" name="s" type="text"/>
+    <param default="s" label="Select the improving method.  h=hierarchical, s=score_based. (-ip)" name="ip" type="text"/>
+    <param label="Amount of maximal terrain resets, until the best solution is retuned as solution. (-r)" name="r" type="integer" value="5"/>
+    <param label="Delimits the convergence count criterion for a reset. (-CC)" name="CC" type="integer" value="130"/>
+    <param label="Delimits the amount of internal ants for termination convergence criterion for a reset. (-aTC)" name="aTC" type="integer" value="50"/>
+    <param checked="false" label="Switch to pseudoknot based prediction using pKiss. Check the pseudoknot parameter usage!!! (-p)" name="p" type="boolean" truevalue="-p" falsevalue=""/>
+    <param checked="false" label="Enable optimized parameters for the usage of pseudo knots (Further parameter input ignored). (-pkPar)" name="pkPar" type="boolean" truevalue="-pkPar" falsevalue=""/>
+    <param default="A" label="Defining the pKiss folding strategy. (--strategy)" name="strategy" type="text"/>
+    <param label="Provides a maximum tGC value [0,1] for the case of uniform distribution sampling. The regular tGC value serves as minimum value. (-tGCmax)" name="tGCmax" type="float" value="-1.0"/>
+    <param label="Provides a tGC variance (sigma square) for the case of normal distribution sampling. The regular tGC value serves as expectation value (mu). (-tGCvar)" name="tGCvar" type="float" value="-1.0"/>
+    <param label="Provides a temperature for the folding algorithms. (-t)" name="t" type="float" value="37.0"/>
+    <param default="" label="Changes the energy parameterfile of RNAfold. If using this explicitly, please provide a suitable energy file delivered by RNAfold.  (-P)" name="P" type="text"/>
+    <param default="STDOUT" label="Provide a path and an output file, e.g. &quot;/path/to/the/target_file&quot;.  (-of)" name="of" type="text"/>
+    <param default="" label="Sequence constraint using RNA nucleotide alphabet {A,C,G,U} and wild-card &quot;N&quot;.  (-Cseq)" name="Cseq" type="text"/>
+    <param label="Sets the level of allowed influence of sequence constraint on the structure constraint [0:no influence; 3:extensive influence]. (-l)" name="l" type="integer" value="1"/>
+    <param default="antaRNA_" label="Defines a name which is used in the sequence output.  (--name)" name="name" type="text"/>
+    <param label="Sets alpha, probability weight for terrain path influence. [0,1] (-a)" name="a" type="float" value="1.0"/>
+    <param label="Sets beta, probability weight for terrain pheromone influence. [0,1]  (-b)" name="b" type="float" value="1.0"/>
+    <param label="Pheromone evaporation rate.  (-er)" name="er" type="float" value="0.2"/>
+    <param label="Structure constraint quality weighting factor. [0,1] (-Cstrw)" name="Cstrw" type="float" value="0.5"/>
+    <param label="GC content constraint quality weighting factor. [0,1] (-Cgcw)" name="Cgcw" type="float" value="5.0"/>
+    <param label="Sequence constraint quality weighting factor. [0,1] (-Cseqw)" name="Cseqw" type="float" value="1.0"/>
+    <param checked="false" label="Displayes intermediate output. (-v)" name="v" type="boolean" truevalue="-v" falsevalue=""/>
+    <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="txt" hidden="false" name="default"/>
+  </outputs>
+  <help><![CDATA[   
+.
+
+===========================
+antaRNA - ant assembled RNA                                   
+===========================
+  
+- 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 
+
+   
+- For questions and remarks please feel free to contact us at http://www.bioinf.uni-freiburg.de/
+
+Example calls:
+
+- python antaRNA.py --Cstr "...(((...)))..." --tGC 0.5 -n 2
+- python antaRNA.py --Cstr ".........AAA(((...)))AAA........." --tGC 0.5 -n 10 --output_file /path/to/antaRNA_TESTRUN -ov
+- python antaRNA.py --Cstr "BBBBB....AAA(((...)))AAA....BBBBB" --Cseq "NNNNANNNNNCNNNNNNNNNNNGNNNNNNUNNN" --tGC 0.5 -n 10
+	]]></help>
+</tool>
+