comparison emboss_trimest.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: trimest102" name="trimest" version="5.0.0">
  <description>Trim poly-A tails off EST sequences</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>trimest -sequence $input1 -outseq $out_file1 -minlength "$minlength" -mismatches "$mismatches" -reverse $reverse -tolower $tolower -fiveprime $fiveprime -osformat2 $out_format1
  -auto</command>
  <inputs>
    <param format="fasta" name="input1" type="data">
      <label>Sequences</label>
    </param>
    <param name="minlength" type="text" value="4">
      <label>Minimum length that a poly-A (or poly-T) tail must have before it is removed</label>
    </param>
    <param name="mismatches" type="text" value="1">
      <label>Number of fewer mismatched non-A bases in a poly-A tail</label>
    </param>
    <param name="reverse" type="select">
      <label>Change the sequence to the forward sense when it is written out</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="tolower" type="select">
      <label>Mask poly-A by converting to lowercase</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="fiveprime" type="select">
      <label>Inspect 5' end of the sequence for poly-T tails</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="out_format1" type="select">
      <label>Output Sequence File Format</label>
      <option value="fasta">FASTA (m)</option>
      <option value="acedb">ACeDB (m)</option>
      <option value="asn1">ASN.1 (m)</option>
      <option value="clustal">Clustal (m)</option>
      <option value="codata">CODATA (m)</option>

      <option value="text">Plain sequence (s)</option>
      <option value="treecon">Treecon (m)</option>
    </param>
  </inputs>
  <outputs>
    <data format="fasta" name="out_file1" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="minlength" value="4"/>

      <param name="fiveprime" value="yes"/>
      <param name="out_format1" value="fasta"/>
      <output name="out_file1" file="emboss_trimest_out.fasta"/>
    </test>
  </tests>
  <code file="emboss_format_corrector.py" />
  <help>

.. class:: warningmark

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/trimest.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: trimest102" name="trimest" version="5.0.0.1">
  <description>Trim poly-A tails off EST sequences</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command>trimest -sequence '$input1' -outseq '$out_file1' -minlength $minlength -mismatches $mismatches -reverse $reverse -tolower $tolower -fiveprime $fiveprime -osformat2 $out_format1
  -auto</command>
  <inputs>
    <param name="input1" type="data" format="fasta" label="Sequences" />
    <param name="minlength" type="integer" value="4" label="Minimum length that a poly-A (or poly-T) tail must have before it is removed" />
    <param name="mismatches" type="integer" value="1" label="Number of fewer mismatched non-A bases in a poly-A tail" />
    <param name="reverse" type="select" label="Change the sequence to the forward sense when it is written out">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="tolower" type="select" label="Mask poly-A by converting to lowercase">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="fiveprime" type="select" label="Inspect 5' end of the sequence for poly-T tails">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="out_format1" type="select" label="Output sequence file format">
      <option value="fasta">FASTA (m)</option>
      <option value="acedb">ACeDB (m)</option>
      <option value="asn1">ASN.1 (m)</option>
      <option value="clustal">Clustal (m)</option>
      <option value="codata">CODATA (m)</option>

      <option value="text">Plain sequence (s)</option>
      <option value="treecon">Treecon (m)</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_file1" format="fasta" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="minlength" value="4"/>

      <param name="fiveprime" value="yes"/>
      <param name="out_format1" value="fasta"/>
      <output name="out_file1" file="emboss_trimest_out.fasta"/>
    </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/trimest.html
  </help>
  <expand macro="citations" />
</tool>