1 <tool id="EMBOSS: eprimer3" name="eprimer3" version="5.0.0">
   2   <description>Picks PCR primers and hybridization oligos and convert it to tabular</description>
   3   <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
   4   <command interpreter="python">
   5       eprimer3.py 
   6           -sequence $input1 
   7           -outfile $out_file1
   8           -numreturn $numreturn
   9           -gcclamp $gcclamp
  10           -osize $osize
  11           -minsize $minsize
  12           -maxsize $maxsize
  13           -otm $otm
  14           -mintm $mintm
  15           -maxtm $maxtm
  16           -maxdifftm $maxdifftm
  17           -ogcpercent $ogcpercent
  18           -mingc $mingc
  19           -maxgc $maxgc
  20           -saltconc $saltconc
  21           -dnaconc $dnaconc
  22           $hybridprobe
  23   </command>
  24   <inputs>
  25     <param format="fasta" name="input1" type="data">
  26       <label>Sequences</label>
  27     </param>
  28     <param name="hybridprobe" label="Hybrid probe" help="An internal oligo is intended to be used as a hybridization probe" type="boolean" truevalue="-hybridprobe" falsevalue="" checked="False" />
  29     <param name="numreturn" label="Number of results" help="Maximum number of primer pairs to return" type="integer" value="5"/>
  30     <param name="gcclamp" label="GC clamp" help="Number of consecutive Gs and Cs at 3' end of both the forward and reverse primer" type="integer" value="0"/>
  31     <param name="osize" label="Optimum size" help="Optimum length of a primer oligo" type="integer" value="20"/>
  32     <param name="minsize" label="Min size" help="Minimum acceptable length of a primer" type="integer" value="18"/>
  33     <param name="maxsize" label="Max size" help="Maximum acceptable length of a primer" type="integer" value="27"/>
  34     <param name="otm" label="Optimum tm" help="Optimum melting tempreture" type="float" value="60.0"/>
  35     <param name="mintm" label="Minimum tm" help="Minimum melting tempreture" type="float" value="57.0"/>
  36     <param name="maxtm" label="Maximum tm" help="Maximum melting tempreture" type="float" value="63.0"/>
  37     <param name="maxdifftm" label="Maximum difftm" help="Maximum acceptable difference between the melting tempertures of the forward and reverse primers" type="float" value="100.0"/>
  38     <param name="ogcpercent" label="Optimum GC%" help="Primer optimum GC percent" type="float" value="50.0"/>
  39     <param name="mingc" label="Minimum GC%" help="Minimum allowable GC percent" type="float" value="20.0"/>
  40     <param name="maxgc" label="Maximum GC%" help="Maximum allowable GC percent" type="float" value="80.0"/>
  41     <param name="saltconc" label="Salt concentration" help="The millimolar concentration of salt in the PCR." type="float" value="50.0"/>
  42     <param name="dnaconc" label="DNA concentration" help="Nanomolar concentration of annealing oligos in the PCR" type="float" value="50.0"/>
  43     <param name="maxpolyx" label="Maximum allowable polyx" help="Maximum allowable length of a mononucleotide repeat in a primer, for example AAAAA" type="integer" value="5"/>
  44     <param name="productsize" label="Optimum product size" help="Optimum size for the PCR product. 0 indicates that there is no optimum product size" type="integer" value="200"/>
  45   </inputs>
  46   <outputs>
  47     <data format="tabular" name="out_file1" />
  48   </outputs>
  49   <tests>
  50     <test>
  51       <param name="input1" value="2.fasta"/>
  52       <output name="out_file1" file="emboss_revseq_out.fasta"/>
  53     </test>
  54   </tests>
  55   <code file="emboss_format_corrector.py" />
  56   <help>
  57 
  58 .. class:: warningmark
  59 
  60 The input dataset needs to be sequences.
  61 
  62 -----
  63 
  64     You can view the original documentation here_.
  65     
  66     .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/eprimer3.html
  67   </help>
  68 </tool>