<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="1.7.1">numpy</requirement>
    <requirement type="package" version="2.1.5">vienna_rna</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
$ov
$v
> $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="fasta" hidden="false" name="default">
        <change_format>
            <when input="v" value="-v" format="txt" />
            <when input="ov" value="-ov" format="txt" />
        </change_format>
    </data>
  </outputs>
  <tests>
    <test>
      <param name="Cstr" value="((..(..((...)))..))" />
      <param name="tGC" value="0.5" />
      <param name="n" value="1" />
      <output name="default">
        <assert_contents>
          <has_text_matching expression="[ACGU]{19}"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <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 parameters:
    - --Cstr "...(((...)))..." --tGC 0.5 -n 2
    - --Cstr ".........AAA(((...)))AAA........." --tGC 0.5 -n 10 --output_file /path/to/antaRNA_TESTRUN -ov
    - --Cstr "BBBBB....AAA(((...)))AAA....BBBBB" --Cseq "NNNNANNNNNCNNNNNNNNNNNGNNNNNNUNNN" --tGC 0.5 -n 10


		]]></help>
  <citations>
  </citations>
</tool>