view emboss_dan.xml @ 10:d49956b87f7e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1

<tool id="EMBOSS: dan19" name="dan" version="5.0.0.1">
  <description>Calculates DNA RNA/DNA melting temperature</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' dan -sequence '$input1' -windowsize $window -goutfile '$out_file1' -graph png -plot $plot1 -shiftincrement $shift -dnaconc $dnaconc
  -saltconc $saltconc -product $product -formamide $formamide -mismatch $mismatch -prodlen $prodlen -thermo $thermo -temperature $temperature -rna $rna -outfile $out_file1 -auto</command>
  <inputs>
    <param name="input1" type="data" format="data" label="On query" />
    <param name="window" type="integer" value="20" label="Window size" />
    <param name="shift" type="integer" value="1" label="Step size (shift increment)" />
    <param name="dnaconc" type="float" value="50.0" label="DNA Concentration (nM)" />
    <param name="saltconc" type="float" value="50.0" label="Salt concentration (mM)" />
    <param name="thermo" type="select" label="Output the DeltaG, DeltaH and DeltaS values">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="temperature" type="float" value="25.0" label="Temperature at which to calculate the DeltaG, DeltaH and DeltaS values" />
    <param name="rna" type="select" label="Sequence is RNA">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="product" type="select" label="Include percent formamide, percent of mismatches allowed and product length">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="formamide" type="float" value="0.0" label="Formamide concentration (nM)" />
    <param name="mismatch" type="float" value="0.0" label="Percent mismatch to be used in calculations" />
    <param name="prodlen" type="integer" value="20" label="Product length to be used in calculations" />
    <param name="plot1" type="select" label="Create a graph">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_file1" format="dan" />
  </outputs>
  <!--
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="window" value="20"/>
      <param name="shift" value="1"/>
      <param name="dnaconc" value="50"/>
      <param name="saltconc" value="50"/>
      <param name="thermo" value="yes"/>
      <param name="temperature" value="25"/>
      <param name="rna" value="no"/>
      <param name="product" value="no"/>
      <param name="formamide" value="0"/>
      <param name="mismatch" value="0"/>
      <param name="prodlen" value="20"/>
      <param name="plot1" value="yes"/>
      <output name="out_file1" file="emboss_dan_out.png"/>
    </test>
  </tests>
  -->
  <help>
    You can view the original documentation here_.

    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/dan.html
  </help>
  <expand macro="citations" />
</tool>