comparison rgWebLogo3.xml @ 1:d16cc2d33359 draft

planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

0:f64b81fda062

<tool id="rgweblogo3" name="Sequence Logo" version="0.4">
   <description>generator for fasta (eg Clustal alignments)</description>
   <requirements>
      <requirement type="package" version="3.3">weblogo</requirement>
      <requirement type="package" version="9.10">ghostscript</requirement>
   </requirements>
   <command interpreter="python"> 
    rgWebLogo3.py -F $outformat -s $size -i $input -o $output -t "$logoname" -c "$colours" -U "$units"

#end if
    </command>
  <inputs>
   <page>
    <param format="fasta" name="input" type="data" label="Fasta File" />
    <param name="logoname" label="Title for output Sequence Logo" type="text" size="50" value="Galaxy-Rgenetics Sequence Logo" />
    <param name="outformat" type="select" label="Output format for image (or text report)" >
      <option value="png" selected="True">PNG screen quality</option>
      <option value="png_print">High quality printable PNG</option>
      <option value="pdf">PDF</option>
      <option value="jpeg">JPG</option>
      <option value="eps">EPS</option>
      <option value="txt">Text (shows the detailed calculations for each position - no image)</option>
    </param>
    <param name="units" type="select" label="Display Units"
      help="What the height of each logo element depicts - eg bits of entropy (default)">
      <option value="bits" selected="True">Entropy (bits)</option>
      <option value="probability">Probability</option>

          <option value="part">Only use a part of the sequence</option>
        </param>
        <when value="complete">
        </when>
        <when value="part">    
           <param name="seqstart" size="5" type="integer" value="1" help="WARNING: Specifying indexes outside the sequence lengths will cause unpredictable but bad consequences!" 
             label="Index (eg 1=first letter) of the start of the sequence range to include in the logo">
           </param>
           <param name="seqend" size="5" type="integer" value="99999" label="Index (eg 75=75th letter) of the end of the sequence range to include in the logo" >
           </param> 
        </when>
    </conditional>
    <param name="size" type="select" label="Output weblogo size" >
      <option value="large" selected="True">Large</option>

       <change_format>
           <when input="outformat" value="png_print" format="png" />
           <when input="outformat" value="png" format="png" />
           <when input="outformat" value="jpeg" format="jpg" />
           <when input="outformat" value="eps" format="eps" />
           <when input="outformat" value="txt" format="txt" />
       </change_format>
    </data>
  </outputs>
  <tests>
    <test>  

1:d16cc2d33359

<tool id="rgweblogo3" name="Sequence Logo" version="0.4">
   <description>generator for fasta (eg Clustal alignments)</description>
   <requirements>
      <requirement type="package" version="1.7.1">numpy</requirement>
      <requirement type="package" version="3.3">weblogo</requirement>
      <requirement type="package" version="9.10">ghostscript</requirement>
   </requirements>
   <command interpreter="python"> 
    rgWebLogo3.py -F $outformat -s $size -i $input -o $output -t "$logoname" -c "$colours" -U "$units"

#end if
    </command>
  <inputs>
   <page>
    <param format="fasta" name="input" type="data" label="Fasta File" />
    <param name="logoname" label="Title for output Sequence Logo" type="text" value="Galaxy-Rgenetics Sequence Logo" />
    <param name="outformat" type="select" label="Output format for image (or text report)" >
      <option value="png" selected="True">PNG screen quality</option>
      <option value="png_print">High quality printable PNG</option>
      <option value="pdf">PDF</option>
      <option value="jpeg">JPG</option>
      <option value="eps">EPS</option>
      <option value="logodata">Text (shows the detailed calculations for each position - no image)</option>
    </param>
    <param name="units" type="select" label="Display Units"
      help="What the height of each logo element depicts - eg bits of entropy (default)">
      <option value="bits" selected="True">Entropy (bits)</option>
      <option value="probability">Probability</option>

          <option value="part">Only use a part of the sequence</option>
        </param>
        <when value="complete">
        </when>
        <when value="part">    
           <param name="seqstart" type="integer" value="1" help="WARNING: Specifying indexes outside the sequence lengths will cause unpredictable but bad consequences!" 
             label="Index (eg 1=first letter) of the start of the sequence range to include in the logo">
           </param>
           <param name="seqend" type="integer" value="99999" label="Index (eg 75=75th letter) of the end of the sequence range to include in the logo" >
           </param> 
        </when>
    </conditional>
    <param name="size" type="select" label="Output weblogo size" >
      <option value="large" selected="True">Large</option>

       <change_format>
           <when input="outformat" value="png_print" format="png" />
           <when input="outformat" value="png" format="png" />
           <when input="outformat" value="jpeg" format="jpg" />
           <when input="outformat" value="eps" format="eps" />
           <when input="outformat" value="logodata" format="txt" />
       </change_format>
    </data>
  </outputs>
  <tests>
    <test>