comparison emboss_einverted.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: einverted28" name="einverted" version="5.0.0">
  <description>Finds DNA inverted repeats</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>einverted -sequence $input1 -outfile $out_file1 -gap $gap -threshold $threshold -match $match -mismatch $mismatch -maxrepeat $maxrepeat -auto</command>
  <inputs>
    <param format="fasta" name="input1" type="data">
      <label>On query</label>
    </param>
    <param name="gap" type="text" value="12">
      <label>Gap penalty</label>
    </param>
    <param name="threshold" type="text" value="50">
      <label>Minimum score threshold</label>
    </param>
    <param name="match" type="text" value="3">
      <label>Match score</label>
    </param>
    <param name="mismatch" type="text" value="-4">
      <label>Mismatch score</label>
    </param>
    <param name="maxrepeat" type="text" value="2000">
      <label>Maximum separation between the start of repeat and the end of the inverted repeat</label>
    </param>
  </inputs>
  <outputs>
    <data format="einverted" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="1.fasta"/>
      <param name="gap" value="12"/>

The input dataset needs to be sequences.

-----

    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/einverted.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. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_

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. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_
  </help>
</tool>

11:0e2484b6829b

<tool id="EMBOSS: einverted28" name="einverted" version="5.0.0.1">
  <description>Finds DNA inverted repeats</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command>einverted -sequence '$input1' -outfile '$out_file1' -gap $gap -threshold $threshold -match $match -mismatch $mismatch -maxrepeat $maxrepeat -auto</command>
  <inputs>
    <param name="input1" type="data" format="fasta" label="On query" />
    <param name="gap" type="integer" value="12" label="Gap penalty" />
    <param name="threshold" type="integer" value="50" label="Minimum score threshold" />
    <param name="match" type="integer" value="3" label="Match score" />
    <param name="mismatch" type="integer" value="-4" label="Mismatch score" />
    <param name="maxrepeat" type="integer" value="2000" label="Maximum separation between the start of repeat and the end of the inverted repeat" />
  </inputs>
  <outputs>
    <data name="out_file1" format="einverted" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="1.fasta"/>
      <param name="gap" value="12"/>

The input dataset needs to be sequences.

-----

    You can view the original documentation here_.

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