comparison emboss_newseq.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: newseq59" name="newseq" version="5.0.0">
  <description>Type in a short new sequence</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>
  <![CDATA[
    newseq
      -outseq '$out_file1'
      -name '$seqname'
      -description '$description'
      -type '$type' 
      -sequence '$sequence'
      -osformat5 '$out_format1'
      -auto
  ]]>
  </command>
  <inputs>
    <param name="seqname" type="text" value="">
      <label>Name of of the sequence</label>
    </param>
    <param name="description" type="text" value="">
      <label>Description of the sequence</label>
    </param>
    <param name="type" type="select">
      <label>Type of sequence</label>
      <option value="N">Nucleic</option>
      <option value="P">Protein</option>
    </param>
    <param name="sequence" type="text" value="">
      <label>The sequence itself</label>
    </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="seqname" value="cytoc"/>
      <param name="description" value="fragment_of_cytochrome_c"/>

      <param name="sequence" value="KKKEERADLIAY"/>
      <param name="out_format1" value="fasta"/>
      <output name="out_file1" file="emboss_newseq_out.fasta"/>
    </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/newseq.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: newseq59" name="newseq" version="5.0.0">
  <description>Type in a short new sequence</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command>
  <![CDATA[
    newseq
      -outseq '$out_file1'
      -name '$seqname'
      -description '$description'
      -type $type
      -sequence '$sequence'
      -osformat5 $out_format1
      -auto
  ]]>
  </command>
  <inputs>
    <param name="seqname" type="text" value="" label="Name of of the sequence" />
    <param name="description" type="text" value="" label="Description of the sequence" />
    <param name="type" type="select" label="Type of sequence">
      <option value="N">Nucleic</option>
      <option value="P">Protein</option>
    </param>
    <param name="sequence" type="text" value="" label="The sequence itself" />
    <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="seqname" value="cytoc"/>
      <param name="description" value="fragment_of_cytochrome_c"/>

      <param name="sequence" value="KKKEERADLIAY"/>
      <param name="out_format1" value="fasta"/>
      <output name="out_file1" file="emboss_newseq_out.fasta"/>
    </test>
  </tests>
  <help>
    You can view the original documentation here_.

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