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 -- *Uma Saxena*
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/