view GEOQuery.xml @ 0:f32198f08f27 draft default tip

Imported from capsule None

<tool id="GEOQuery" name="GEOQuery">
	<description>GEOQuery wrapper</description>
	<requirements>
	  <container type="docker">sblanck/smat</container>
	</requirements>
	<command>
		/galaxy-tools/stderr_wrapper.py Rscript 
		/galaxy-tools/transcriptomics/GEOquery/GEOQuery.R 
		$GEOQueryID 
		$GEOQueryData 
		$GEOQueryRData 
		$conditions
		$transformation
	</command>

	<inputs>
		<param name="GEOQueryID" type="text" size="12" optional="false" label="GEOQuery ID" help="">
			<validator type="empty_field"/>
		</param>
	<param name="transformation" type="select" label="log2 transformation">
			<option value="auto">auto</option>
            <option value="yes">yes</option>
            <option value="no">no</option>
        </param>
	</inputs>

	<outputs>
		<data format="tabular" name="GEOQueryData" label="GEOQuery Data of ${GEOQueryID}"/>
		<data format="cond" name="conditions" label="conditions of ${GEOQueryID}"/>
        <data format="rdata" name="GEOQueryRData" label="GEOQuery RData of ${GEOQueryID}"/>		
	</outputs>
<help>
**What it does**     	

This tool fetches microarray data directly from GEO database, based on the GEOQuery R package. Given a GSE accession ID, it returns an Rdata object containing the data and a text file (.cond file) summarizing the conditions of the experiment. 
The .cond file is a text file containing one line per sample in the experiment. Each line is made of 3 columns:

	- Sample ID 
	- Condition of the biological sample
	- Description of the biological sample

**Example** of .cond file      	
::

 Sample ID 	Condition			Description
 GSM80460	series of 16 tumors	GSM80460 OSCE-2T SERIES OF 16 TUMORS
 GSM80461	series of 16 tumors	GSM80461 OSCE-4T Series of 16 Tumors
 GSM80462	series of 16 tumors	GSM80462 OSCE-6T Series of 16 Tumors
 GSM80476	series of 4 normals	GSM80476 OSCE-2N Series of 4 Normals
 GSM80477	series of 4 normals	GSM80477 OSCE-9N Series of 4 Normals
    
**Results**
	
- Rdata object containing data for further analysis
- Condition (.cond) file summarizing conditions of the experiment
- Tabular (.txt) file containing expression data for each sample
  		

</help>


</tool>