comparison emboss_checktrans.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: checktrans9" name="checktrans" version="5.0.0">
  <description>Reports STOP codons and ORF statistics of a protein</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <command>checktrans -sequence $input1 -outfile $out_file1 -outseq $out_file2 -osformat3 $out_format2 -outfeat $out_file3 -offormat4 $out_format3 -orfml $orfml -addlast $addlast -auto</command>
  <inputs>
    <param format="fasta" name="input1" type="data">
      <label>On query</label>
    </param>
    <param name="orfml" type="text" value="100">
      <label>Minimum ORF Length to report</label>
    </param>
    <param name="addlast" type="select">
      <label>An asterisk in the protein sequence indicates the position of a STOP codon. Checktrans assumes that all ORFs end in a STOP codon. Forcing the sequence to end with an asterisk, if there
      is not one there already, makes checktrans treat the end as a potential ORF. If an asterisk is added, it is not included in the reported count of STOPs</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="out_format2" 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="strider">DNA strider (m)</option>
      <option value="swiss">SwisProt entry (m)</option>
      <option value="text">Plain sequence (s)</option>
      <option value="treecon">Treecon (m)</option>
    </param>
    <param name="out_format3" type="select">
      <label>Output Feature File Format</label>
      <option value="gff">GFF</option>
      <option value="embl">EMBL</option>
      <option value="swiss">SwissProt</option>
    </param>
  </inputs>
  <outputs>
    <data format="checktrans" name="out_file1" />
    <data format="fasta" name="out_file2" />
    <data format="gff" name="out_file3" />
  </outputs>
 <!--   <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="orfml" value="100"/>

      <output name="out_file1" file="emboss_checktrans_out1.txt"/>
      <output name="out_file2" file="emboss_checktrans_out2.fasta"/>
      <output name="out_file3" file="emboss_checktrans_out3.gff"/>
    </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/checktrans.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: checktrans9" name="checktrans" version="5.0.0.1">
  <description>Reports STOP codons and ORF statistics of a protein</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command>checktrans -sequence '$input1' -outfile '$out_file1' -outseq '$out_file2' -osformat3 $out_format2 -outfeat '$out_file3' -offormat4 $out_format3 -orfml $orfml -addlast $addlast -auto</command>
  <inputs>
    <param name="input1" type="data" format="fasta" label="On query" />
    <param name="orfml" type="integer" value="100" label="Minimum ORF length to report" />
    <param name="addlast" type="select" label="An asterisk in the protein sequence indicates the position of a STOP codon" help="Checktrans assumes that all ORFs end in a STOP codon. Forcing the sequence to end with an asterisk, if there is not one there already, makes checktrans treat the end as a potential ORF. If an asterisk is added, it is not included in the reported count of STOPs">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="out_format2" 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="strider">DNA strider (m)</option>
      <option value="swiss">SwisProt entry (m)</option>
      <option value="text">Plain sequence (s)</option>
      <option value="treecon">Treecon (m)</option>
    </param>
    <param name="out_format3" type="select" label="Output feature file format">
      <option value="gff">GFF</option>
      <option value="embl">EMBL</option>
      <option value="swiss">SwissProt</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_file1" format="checktrans" />
    <data name="out_file2" format="fasta" />
    <data name="out_file3" format="gff" />
  </outputs>
 <!--   <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="orfml" value="100"/>

      <output name="out_file1" file="emboss_checktrans_out1.txt"/>
      <output name="out_file2" file="emboss_checktrans_out2.fasta"/>
      <output name="out_file3" file="emboss_checktrans_out3.gff"/>
    </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/checktrans.html
  </help>
  <expand macro="citations" />
</tool>