view rgweblogo/rgWebLogo3.xml @ 0:cec2527697f6

Migrated tool version 0.1 from old tool shed archive to new tool shed repository

<tool id="weblogo3" name="Sequence Logo" version="0.1">
   <description>generator for fasta (eg Clustal alignments)</description>
   <command> 
    weblogo -F $outformat -s $size -f $input -o $output -t "$logoname"
   </command>
  <inputs>
   <page>
    <param format="fasta" name="input" type="data" label="Fasta File" />
    <param name="logoname" label="Name for output logo - will appear on graphics" type="text" size="50" value="Galaxy/Rgenetics weblogo" />
    <param name="outformat" type="select" label="Output weblogo format" >
      <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="size" type="select" label="Output weblogo size" >
      <option value="large" selected="True">Large</option>
      <option value="medium">Medium</option>
      <option value="small">Small</option>
    </param>
   </page>
  </inputs>
  <outputs>
    <data format="pdf" name="output"  label="${logoname}_output.${outformat}">
       <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>
  
      <param name="input" value="rgClustal_testout.fasta" />
      <param name = "logoname" value="Galaxy/Rgenetics weblogo" />
      <param name = "outformat" value="jpeg" />
      <param name = "size" value="medium" />
    
      <output name="output" file="rgWebLogo3_test.jpg" ftype="jpg" />
    </test>

  </tests>
  <help>

**Note**

This tool uses Weblogo3_ in Galaxy to generate a sequence logo. The input file must be a fasta file in your current history.

A typical output looks like this

.. image:: ./static/images/rgWebLogo3_test.jpg

----

**Why use WebLogo in Galaxy?**

Weblogo3_ is a good example of an easy to use tool and there are plenty of other web accessible weblogo generator sites available. 

However, none of those offer the combination of:

1) persistence of analyses and data in multiple shareable histories, pages and libraries 

2) convenient access to shared data libraries, workflows and user controlled pages,  and to 3rd party data sources like UCSC tables. 

3) analyses integrated with many other applicable generic and specialized tools already available for downstream processing.

that you get for free when you use Galaxy. No muss; no fuss.

----

**Attribution**

Weblogo attribution and associated documentation are available at Weblogo3_

This wrapper was written by Ross Lazarus for the rgenetics project and the source code is licensed under the LGPL_ like other rgenetics artefacts

.. _Weblogo3: http://weblogo.berkeley.edu/

.. _LGPL: http://www.gnu.org/copyleft/lesser.html

  </help>

</tool>