Hi,

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 GEOquery. 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>

<inputs>

<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>

</param>

<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" default="0"/> <param name="input_exprs" type="hidden" format="tabular" label="Expression file" default="0"/>

</when>

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" default="0"/> <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> </options>

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

</param> </when>

Any help or suggestion is much appreciated.

Thanks

Uma