Question: Passing/Referencing Arguments From Xml To R Script While Using Xml Conditional Tag
0
Uma Saxena • 10 wrote:
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*