annotate emboss_est2genome.xml @ 10:d49956b87f7e draft

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

<tool id="EMBOSS: est2genome32" name="est2genome" version="5.0.0.1">
  <description>Align EST and genomic DNA sequences</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command>est2genome -estsequence '$input1' -genomesequence '$input2' -outfile '$out_file1' -match $match -mismatch $mismatch -gappenalty $gappenalty -intronpenalty $intronpenalty -splicepenalty
  $splicepenalty -minscore $minscore -reverse $reverse -splice $splice -mode $mode -best $best -shuffle $shuffle -seed $seed -align $align -width $width -auto</command>
  <inputs>
    <param name="input1" type="data" format="fasta" label="EST sequence(s)" />
    <param name="input2" type="data" format="data" label="Genomic sequence" />
    <param name="match" type="integer" value="1" label="Score for matching two bases" />
    <param name="mismatch" type="integer" value="1" label="Cost for mismatching two bases" />
    <param name="gappenalty" type="integer" value="2" label="Cost for deleting a single base in either sequence, excluding introns" />
    <param name="intronpenalty" type="integer" value="40" label="Cost for an intron, independent of length" />
    <param name="splicepenalty" type="integer" value="20" label="Cost for an intron, independent of length and starting/ending on donor-acceptor sites" />
    <param name="minscore" type="integer" value="30" label="Exclude alignments with scores below this threshold score" />
    <param name="reverse" type="select" label="Reverse the orientation of the EST sequence">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="splice" type="select" label="Use donor and acceptor splice sites">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="mode" type="select" label="Comparison mode">
      <option value="both">Both strands</option>
      <option value="forward">Forward strand only</option>
      <option value="reverse">Reverse strand only</option>
    </param>
    <param name="best" type="select" label="Only best comparisons">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="shuffle" type="integer" value="0" label="Shuffle" />
    <param name="seed" type="integer" value="20825" label="Random number seed" />
    <param name="align" type="select" label="Show the alignment">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="width" type="integer" value="50" label="Alignment width" />
  </inputs>
  <outputs>
    <data name="out_file1" format="est2genome" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="input2" value="1.fasta"/>
      <param name="match" value="1"/>
      <param name="mismatch" value="1"/>
      <param name="match" value="1"/>
      <param name="gappenalty" value="2"/>
      <param name="intronpenalty" value="40"/>
      <param name="splicepenalty" value="20"/>
      <param name="minscore" value="30"/>
      <param name="reverse" value="no"/>
      <param name="splice" value="yes"/>
      <param name="mode" value="both"/>
      <param name="best" value="yes"/>
      <param name="shuffle" value="0"/>
      <param name="seed" value="20825"/>
      <param name="align" value="no"/>
      <param name="width" value="50"/>
      <output name="out_file1" file="emboss_est2genome_out.est2genome"/>
    </test>
  </tests>
  <help>
.. class:: warningmark

The input dataset needs to be sequences.

-----

    You can view the original documentation here_.

    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/est2genome.html
  </help>
  <expand macro="citations" />
</tool>