--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/carpet-src-1/tools/CARPET/calcolo_p_v4_norm.xml	Tue Jun 07 16:50:41 2011 -0400
@@ -0,0 +1,187 @@
+<tool id="expressions" name="TEA" version="1.0.0">
+  <description>Tiling Expression Analizer</description>
+  <command interpreter="perl">calcolo_p_v4_norm_intron.pl -opt ${ann_choice.type1} -log ${ann_choice.type_data} -ann ${ann_choice.ann} -wt ${ann_choice.wt} -treat ${ann_choice.treat} -out $output -fdr ${ann_choice.fdr} -pv ${ann_choice.pv} -norm ${ann_choice.norm} -rc ${ann_choice.rc} -fc ${ann_choice.summary_choice.fc} -exon ${ann_choice.type} -sum_met ${ann_choice.summary_choice.fc_output}</command>
+  <inputs>
+  <conditional name="ann_choice">
+   	<param name="type1" type="select" label="Analysis type">
+   	  <option value="comp">comparison</option>
+   	  <option value="expr">expression</option>
+  	</param>
+  	
+    <when value="comp">
+   	   	<param format="tabular" name="ann" type="data" label="annotation file"/>
+    	<param format="tabular" name="wt" type="data" label="expression chip condition A"/>
+    	<param format="tabular" name="treat" type="data" label="expression chip condition B"/>
+    	<param name="type_data" type="select" label="Data type">
+      		<option value="log">log2 value</option>
+   			<option value="no_log">raw value</option>
+      	</param>
+    	<param name="norm" type="select" label="Normalization">
+      		<option value="yes">quantile-normalization</option>
+   			<option value="no">no normalization</option>
+      	</param>
+      	<param name="type" type="select" label="probes selection">
+      		<option value="internal_exon">internal exon</option>
+      		<option value="all_exon">all exon</option>
+      		<option value="last_exon">last exon</option>
+     	</param>
+     	<conditional name="summary_choice">
+     		<param name="fc_output" type="select" label="summary method">
+     			<option value="mean">mean</option>
+      			<option value="median">median</option>
+      			<option value="both">both</option>
+      		</param>
+      		 <when value="mean">
+      		 	<param name="fc" size="3" type="text" value="1.5" label="Fold change cutoff"/>
+      		 </when>
+      		 <when value="median">
+      		 	<param name="fc" size="3" type="text" value="1.5" label="Fold change cutoff"/>
+      		 </when>
+      		 <when value="both">
+      		 	<param name="fc" size="12" type="text" value="NOT-NEEDED" label="Fold change cutoff"/>
+      		 </when>
+      	</conditional>	 
+    	<param name="rc" size="2" type="text" value="7" label="raw value cutoff (log2)"/>
+    	<param name="fdr" type="select" label="FDR correction">
+      		<option value="yes">yes</option>
+      		<option value="no">no</option>
+      	</param>	
+    	<param name="pv" size="4" type="text" value="0.05" label="p-value cutoff"/>
+    	
+   		
+   		
+   	</when>	
+   	  	<when value="expr">
+   	  			 	<param format="tabular" name="ann" type="data" label="annotation file"/>
+    				<param format="tabular" name="wt" type="data" label="expression chip"/>
+    				<param format="tabular" name="treat" type="data" label="NOT NEEDED"/>
+    				<param name="type_data" type="select" label="Data type">
+      					<option value="log">log2 value</option>
+   						<option value="no_log">raw value</option>
+      				</param>
+    				<param name="type" type="select" label="probes selection">
+      					<option value="internal_exon">internal exon</option>
+      					<option value="all_exon">all exon</option>
+      					<option value="last_exon">last exon</option>
+     				</param>
+     				<conditional name="summary_choice">
+     					<param name="fc_output" type="select" label="summary method">
+     						<option value="mean">mean</option>
+      						<option value="median">median</option>
+      						<option value="both">both</option>
+      					</param>
+      				 	 <when value="mean">
+      					 	<param name="fc" size="12" type="text" value="NOT-NEEDED" label="Fold change cutoff"/>
+     			 		 </when>
+     			 		 <when value="median">
+      					 	<param name="fc" size="12" type="text" value="NOT-NEEDED" label="Fold change cutoff"/>
+     			 		 </when>
+     			 		 <when value="both">
+      					 	<param name="fc" size="12" type="text" value="NOT-NEEDED" label="Fold change cutoff"/>
+      					 </when>
+     			 	</conditional>
+     				<param name="norm" size="12" type="text" value="NOT-NEEDED" label="Normalization"/>
+    				<param name="pv" size="12" type="text" value="NOT-NEEDED" label="p-value cutoff"/>
+    				<param name="fdr" size="12" type="text" value="NOT-NEEDED" label="FDR correction"/>
+    				<param name="rc" size="12" type="text" value="NOT-NEEDED" label="raw value cutoff (log2)"/>   
+   		</when>
+   	</conditional>
+      
+  
+  </inputs>
+  <outputs>
+    <data format="tabular" name="output" />
+  </outputs>
+
+  <help>
+ .. class:: infomark
+
+**What it does**
+
+TEA utilizes NimbleGen expression files in gff format and annotated table by ENO as INPUT FILES and generates a table with the expression value. When comparing two different conditions a Fold Change and a p-value are calculated.
+
+PLEASE, for more detailed information refer to the CARPET user Manual:
+click to download_ it.
+
+.. _download: /static/example_file/CARPET_userManual.zip
+
+--------
+
+**Parameters:**
+
+- **Analysis type:** 
+                     - **expression** analysis calculates an expression value for each transcript coming from the mean or the median of all matching probes
+                     - **comparison** analysis calculate an expression value for each transcript in both conditions, then calculates a Fold Change for each transcript and a p-value based on t-Test distribution. 
+- **Data type:** 
+    - **log2 value:** the data is not converted in log2
+    - **raw value:** the data is converted in log2
+- **Normalization:** quantile normalization between the two chips (not necessary if analysis type is "expression")
+- **probe selection:** 
+	- **internal exon:** only probes annotated as exons are used to calculate expression value.
+	- **all exon:** also probes annotated at the boundaries of introns/exons are used to calculate the expression value. (probes in intronexon position usually have lower signal)
+	- **last exon:** only probes in the last exon are used to calculate expression value. This analysis can be preferred for cDNA generated by oligo-dT RT, since 3' of transcripts are generally better represented.
+- **summary method:** 
+	- **mean:** fold change for each gene is calculated based on the mean value
+	- **median:** fold change for each gene is calculated based on the median value
+	- **both:** both are used
+- **Fold change cutoff:** only transcripts with FC higher than cutoff are kept 
+- **FDR:**
+	- **yes:** False Discovery Rate correction is applied (as described in Storie et al. 2002)
+	- **no:** No correction --> raw p-value
+- **p-value cutoff:** only transcripts with p-value less than cutoff are kept 
+- **raw value cutoff (log2):** only transcripts with raw value higher than cutoff at least in one experiment are kept 
+
+--------
+
+
+**INPUT FILE**
+
+Nimblegen gives you back a GFF file with the coordinates of each probe and the signal raw value.
+
+Click here_ to download a GFF file example.
+
+.. _here: /static/example_file/Expression_analysis_files.zip
+
+
+Example of Nimblegen Expression GFF format::
+
+    chr19  Nimblegen  tiling_array  100000  1000051  20459	 +   .  probe_name
+    chr19  Nimblegen  tiling_array  100100  1000151   1394	 +   .  probe_name
+
+.. class:: warningmark
+
+The sixth column **must** contain the raw signal (**NOT** log2) that Nimblegen gives you back after the experiment
+
+The annotation table **MUST** be created usign ENO tool, before running TEA.
+
+---------
+
+.. class:: infomark
+
+**How does it work?**
+
+For each gene is built the signal distibution of the probes matching Exon.
+
+-In an expression experiment, the mean or the median of the distribution represents the result of Tea.
+
+-In a comparison experiment the distibution of the gene exon signal is compared between the two conditions (1 and 2) and a t-test is performed with the possibility to introduce FDR correction.
+
+.. image:: static/images/CARPET/Tea.png
+
+
+
+
+**OUTPUT**
+
+- **expresion**
+
+.. image:: static/images/CARPET/expression.png
+
+- **comparison**
+
+.. image:: static/images/CARPET/comparison.png
+
+ </help>
+  
+
+</tool>