This may appear as a very basic question.

I:  I have in the past used "name" as the object that allows the argument
reference to passed from XML to Rscript running in the background. However I
am currently using a conditional tag that makes this
slightly incomprehensible. My command line argument for Rscript is given in
the <command> tag. I have also tried to define Rscript reference by using
XML filter tags "key" or "ref" but perhaps this is the wrong way to go.

Argument $geoID is a text reference that that the user writes in. This ID is
read into Rscript and within the script, I access the data using R package
Argument $input_cel allows the user to upload a CEL file
Argument $input_cel allows the user to upload a text tab limited file

Codes are given below. The error I get on the galaxy interface is "NotFound:
cannot find 'geoID'"

<tool id="testtool" name="TEST">

  <description> xyz </description>

  <command>ppgalaxy.r $input $geoID $input_cel $input_exprs $platform
$species $exptRecords_dist $exptRecords_consensus
$exptRfingerprintTOconsensus $distHistogram</command>


  <param name="input" type="select" label="User Data Source"/>

  <conditional name="input">

        <param name="input_type" type="select" data_key="input" label="User
Data Type">

         <option value="GEO_data" selected="true">GSM ID</option>
         <option value="cel.file" >CEL file Upload</option>
         <option value="data.exprs" >Expression Vector Upload</option>


     <when value="GEO_data">
         <param name="geoID" label="GEO id by GSM" type="text" area="TRUE"
size="7" />
         <param name="input_cel" type="hidden" label="CEL file"
         <param name="input_exprs" type="hidden" format="tabular"
label="Expression file" default="0"/>


II. I call a param's tag within a param's, My codes are given below. The
problem is, I should be able to read in three arguments (1) input_exprs :
data file (2) platform name (3) selected Species. On the GUI, the platform
and species is not visible

<when value="data.exprs">
        <param name="geoID" type="hidden" label="GEO id by GSM"
        <param name="input_cel" type="hidden" label="CEL file" default="0"/>
         <param name="input_exprs" format="tabular" label="Expression file"
type="data" >

         <options name="Platform by GPL" type="text" size="7"
value="platform" >
       <label>Platform Input - GPL </label>

        <param name="species" type="select" format="text">
     <option value="human">HOMO SAPIENS</option>
     <option value="mouse">MUS MUSCULUS</option>


Any help or suggestion is much appreciated.


*Uma Saxena*
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