comparison emboss_dan.xml @ 11:0e2484b6829b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68

10:9b98d3d903c6

<tool id="EMBOSS: dan19" name="dan" version="5.0.0">
  <description>Calculates DNA RNA/DNA melting temperature</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command interpreter="perl">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 format="data" name="input1" type="data">
      <label>On query</label>
    </param>
    <param name="window" type="text" value="20">
      <label>Window Size</label>
    </param>
    <param name="shift" type="text" value="1">
      <label>Step size (shift increment)</label>
    </param>
    <param name="dnaconc" type="text" value="50.0">
      <label>DNA Concentration (nM)</label>
    </param>
    <param name="saltconc" type="text" value="50.0">
      <label>Salt concentration (mM)</label>
    </param>
    <param name="thermo" type="select">
      <label>Output the DeltaG, DeltaH and DeltaS values</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="temperature" type="text" value="25 ">
      <label>Temperature at which to calculate the DeltaG, DeltaH and DeltaS values</label>
    </param>
    <param name="rna" type="select">
      <label>Sequence is RNA</label>
      <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</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="formamide" type="text" value="0 ">
      <label>Formamide concentration (nM)</label>
    </param>
    <param name="mismatch" type="text" value="0 ">
      <label>Percent mismatch to be used in calculations</label>
    </param>
    <param name="prodlen" type="text" value="20">
      <label>Product length to be used in calculations</label>
    </param>
    <param name="plot1" type="select">
      <label>Create a graph</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
  </inputs>
  <outputs>
    <data format="dan" name="out_file1" />
  </outputs>
  <!--
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>

      <param name="plot1" value="yes"/>
      <output name="out_file1" file="emboss_dan_out.png"/>
    </test>
  </tests>
  -->
  <code file="emboss_format_corrector.py" />
  <help>
    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dan.html

------

**Citation**

For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_

If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
  </help>
</tool>

11:0e2484b6829b

<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="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>