XML file for galaxy tool

RNASeq.xml

<tool id="RNASeq" name="RNASeq tool" version="0.99.0">
  <description>Description goes here</description>
  <command interpreter="bash">Rscript_wrapper.sh /Users/dtenenba/dev/galaxy-dist/tools/bioc/RNASeq.R $countsTsv $designTsv "$organism" $dispersion $minimumCountsPerMillion $minimumSamplesPerTranscript $out_file1 $out_file2</command>
  <inputs>
    <param name="countsTsv" type="data" format="tabular" label="Counts TSV File:"/>
    <param name="designTsv" type="data" format="tabular" label="Design TSV File:"/>
    
    <param name="organism" type="select" label="Organism">
        <option value="Anopheles">Anopheles</option>
        <option value="Arabidopsis">Arabidopsis</option>
        <option value="Bovine">Bovine</option>
        <option value="Worm">Worm</option>
        <option value="Canine">Canine</option>
        <option value="Fly">Fly</option>
        <option value="Zebrafish">Zebrafish</option>
        <option value="Chicken">Chicken</option>
        <option value="Human">Human</option>
        <option value="Mouse">Mouse</option>
        <option value="Rhesus">Rhesus</option>
        <option value="Malaria">Malaria</option>
        <option value="Chimp">Chimp</option>
        <option value="Rat">Rat</option>
        <option value="Yeast">Yeast</option>
        <option value="Streptomyces coelicolor">Streptomyces coelicolor</option>
        <option value="Pig">Pig</option>
        <option value="Xenopus">Xenopus</option>    </param>
    <param name="dispersion" type="select" label="Dispersion">
          <option value="Tagwise">Tagwise</option>
          <option value="Common">Common</option>
    </param>
    <param name="minimumCountsPerMillion" type="integer" value="" size="30" label="Minimum counts per million"/>
    <param name="minimumSamplesPerTranscript" type="integer" value="" size="30" label="Minimum samples per transcript"/>

  </inputs>


  <outputs>
    <data format="pdf" name="out_file1" />
    <data format="csv" name="out_file2" />
  </outputs>

    <tests>
        <test>
            <param name="countsTsv" value="counts.txt"/>
            <param name="designTsv" value="design.txt"/>
            <param name="organism" value="Fly"/>
            <param name="dispersion" value="Tagwise"/>
            <param name="minimumCountsPerMillion" value="1"/>
            <param name="minimumSamplesPerTranscript" value="1"/>
            
            <output name="out_file1" file="MDSPlot.pdf"/>
            <output name="out_file2" file="outputs.csv"/>
        </test>
    </tests>
<help>
.. class:: infomark

CHANGEME This tool allows you to plot values contained in columns of a dataset against each other and also allows you to have different series corresponding to the same or different datasets in one plot.

-----

.. class:: warningmark

CHANGEME This tool throws an error if the columns selected for plotting are absent or are not numeric and also if the lengths of these columns differ.

-----

**CHANGEME Example**

Input file::

    1   68  4.1
    2   71  4.6
    3   62  3.8
    4   75  4.4
    5   58  3.2
    6   60  3.1
    7   67  3.8
    8   68  4.1
    9   71  4.3
    10  69  3.7 

Create a two series XY plot on the above data:

- Series 1: Red Dashed-Line plot between columns 1 and 2
- Series 2: Blue Circular-Point plot between columns 3 and 2 

.. image:: ./static/images/xy_example.jpg
</help>
</tool>