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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/ commit c48d2707acb0e6b6d9dc3aa19d1ce13d7249dc46-dirty

<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="1.8">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
$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="fasta" 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/

	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>