comparison emboss_est2genome.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: est2genome32" name="est2genome" version="5.0.0">
  <description>Align EST and genomic DNA sequences</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></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 format="fasta" name="input1" type="data">
      <label>EST sequence(s)</label>
    </param>
    <param format="data" name="input2" type="data">
      <label>Genomic sequence</label>
    </param>
    <param name="match" type="text" value="1">
      <label>Score for matching two bases</label>
    </param>
    <param name="mismatch" type="text" value="1">
      <label>Cost for mismatching two bases</label>
    </param>
    <param name="gappenalty" type="text" value="2">
      <label>Cost for deleting a single base in either sequence, excluding introns</label>
    </param>
    <param name="intronpenalty" type="text" value="40">
      <label>Cost for an intron, independent of length</label>
    </param>
    <param name="splicepenalty" type="text" value="20">
      <label>Cost for an intron, independent of length and starting/ending on donor-acceptor sites</label>
    </param>
    <param name="minscore" type="text" value="30">
      <label>Exclude alignments with scores below this threshold score</label>
    </param>
    <param name="reverse" type="select">
      <label>Reverse the orientation of the EST sequence</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="splice" type="select">
      <label>Use donor and acceptor splice sites</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="mode" type="select">
      <label>Comparison mode</label>
      <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</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="shuffle" type="text" value="0">
      <label>Shuffle</label>
    </param>
    <param name="seed" type="text" value="20825">
      <label>Random number seed</label>
    </param>
    <param name="align" type="select">
      <label>Show the alignment</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="width" type="text" value="50">
      <label>Alignment width</label>
    </param>
  </inputs>
  <outputs>
    <data format="est2genome" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="input2" value="1.fasta"/>

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/est2genome.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: 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"/>

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>