comparison emboss_sixpack.xml @ 14:27c43fb015f0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753

13:d5c3794bd246

<tool id="EMBOSS: sixpack90" name="sixpack" version="5.0.0.1">
  <!-- tool adds file description and timestamp to output data -->
  <description>Display a DNA sequence with 6-frame translation and ORFs</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command>sixpack -sequence '$input1' -outfile '$ofile1' -outseq '$ofile2' -table $table -firstorf $firstorf -lastorf $lastorf -mstart $mstart -reverse $reverse -orfminsize $orfminsize -uppercase
  '$uppercase' -number $number -width $width -length $length -margin $margin -name $disp_name -description $description -offset $offset -html $html_out1 -osformat $out_format2 -auto</command>
  <inputs>
    <param name="input1" type="data" format="fasta" label="Sequences" />
    <param name="table" type="select" label="Code to use">
      <option value="0">Standard</option>
      <option value="1">Standard (with alternative initiation codons)</option>

    <param name="reverse" type="select" label="Display the translation of the DNA sequence in the 3 reverse frames">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="orfminsize" type="integer" value="1" label="Minimum size of Open Reading Frames (ORFs) to display in the translations" />
    <param name="uppercase" type="text" value="" label="Regions to put in uppercase" />
    <param name="number" type="select" label="Number the sequence at the beginning and the end of each line">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="width" type="integer" value="60" label="Number of nucleotides displayed on each line" />

  </inputs>
  <outputs>
    <data name="ofile1" format="sixpack" />
    <data name="ofile2" format="fasta" />
  </outputs>
<!--    <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="table" value="0"/>
      <param name="firstorf" value="no"/>
      <param name="lastorf" value="no"/>

      <param name="disp_name" value="no"/>
      <param name="description" value="no"/>
      <param name="offset" value="1"/>
      <param name="html_out1" value="no"/>
      <param name="out_format2" value="fasta"/>
      <output name="ofile2" file="emboss_sixpack_out.fasta"/>
    </test>
  </tests> -->
  <help>
.. class:: warningmark

The input dataset needs to be sequences.

14:27c43fb015f0

<tool id="EMBOSS: sixpack90" name="sixpack" version="@VERSION@+galaxy2">
  <!-- tool adds file description and timestamp to output data -->
  <description>Display a DNA sequence with 6-frame translation and ORFs</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command><![CDATA[
    sixpack -sequence '$input1' -outfile '$ofile1' -outseq '$ofile2' -table $table -firstorf $firstorf -lastorf $lastorf -mstart $mstart -reverse $reverse -orfminsize $orfminsize 
    #if str($uppercase):
      -uppercase '$uppercase' 
    #end if  
    -number $number -width $width -length $length -margin $margin -name $disp_name -description $description -offset $offset -html $html_out1 -osformat $out_format2 -auto]]></command>
  <inputs>
    <param name="input1" type="data" format="fasta" label="Sequences" />
    <param name="table" type="select" label="Code to use">
      <option value="0">Standard</option>
      <option value="1">Standard (with alternative initiation codons)</option>

    <param name="reverse" type="select" label="Display the translation of the DNA sequence in the 3 reverse frames">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="orfminsize" type="integer" value="1" label="Minimum size of Open Reading Frames (ORFs) to display in the translations" />
    <param name="uppercase" type="text" value="" label="Regions to put in uppercase" help="If this is left blank, then the sequence case is left alone. A set of regions is specified by a set of pairs of positions. The positions are integers. They are separated by any non-alpha-numeric character. Three examples of region specifications are: 1) 24-45, 56-78 2) 1:45, 67=99;765..888 3) 1,5,8,10,23,45,57,99"/>
    <param name="number" type="select" label="Number the sequence at the beginning and the end of each line">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="width" type="integer" value="60" label="Number of nucleotides displayed on each line" />

  </inputs>
  <outputs>
    <data name="ofile1" format="sixpack" />
    <data name="ofile2" format="fasta" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="table" value="0"/>
      <param name="firstorf" value="no"/>
      <param name="lastorf" value="no"/>

      <param name="disp_name" value="no"/>
      <param name="description" value="no"/>
      <param name="offset" value="1"/>
      <param name="html_out1" value="no"/>
      <param name="out_format2" value="fasta"/>
      <output name="ofile1" file="emboss_sixpack_out2.sixpack" />
      <output name="ofile2" file="emboss_sixpack_out.fasta"/>
    </test>
  </tests>
  <help>
.. class:: warningmark

The input dataset needs to be sequences.