# HG changeset patch
# User sblanck
# Date 1490106349 14400
# Node ID f8a2f1fec8ef06dd0417023e4dfc5563f2b52ad9
# Parent  5a57280b9125df5b362bbdec07626823cf6a1f88
Deleted selected files

diff -r 5a57280b9125 -r f8a2f1fec8ef AffyQCnormalization.xml
--- a/AffyQCnormalization.xml	Thu Nov 10 07:34:57 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,61 +0,0 @@
-<tool id="QCnormalization" name="QCnormalization" version="0.1.0">
-	<description>Quality control and normalization of affymetrix expression data</description>
-	<requirements>
-	  <container type="docker">sblanck/smat</container>
-	</requirements>
-	<command>
-		<![CDATA[
-		/galaxy-tools/stderr_wrapper.py Rscript 
-		/galaxy-tools/transcriptomics/AffyQCnormalization/AffyQCnormalization.R
-		   	#for $input in $inputs
-                "${input}"
-			    "${input.name}"
-     		#end for
-			"${normalization}"
-			$result_export_eset
-       		$result_html
-			$result_html.files_path
-		/galaxy-tools/transcriptomics/AffyQCnormalization/AffyQCnormalization_tpl.html
-		]]>
-		</command>
-	
-		<inputs>
-	
-		<param name="inputs" type="data" format="cel" multiple="true" label=".CEL files" help=".CEL files to be used"/>
-
-		<param name="normalization" type="select" label="Preprocessing/normalization">
-		
-    		<option value="rma">rma (backgroung correction + quantile normalization + log2)</option>
-            <option value="quantile">quantile normalization + log2</option>
-            <option value="background">background correction + log2</option>
-            <option value="log2">log2 only</option>
-           
-		
-		</param>
-		
-	</inputs>
-	<outputs>
-		<data format="rdata" name="result_export_eset" label="export normalized expressionSet"/>		
-		<data format="html" name="result_html" label="QC result"/>
-	</outputs>
-
-	<help>
-<![CDATA[
-		**What it does** 
-		    	
-The QCnormalization tool offers to ensure the quality of the data and to normalize them. Several normalization methods are available :
-
-* rma normalization 
-* quantile normalization + log2
-* background correction + log2
-* log2 only
-
-**Results**
-
-- Several quality figures : microarray images, boxplots and MA plots
-- Rdata object containing the normalized data for further analysis
-  		
-]]>
-</help>
-
-</tool>
\ No newline at end of file
diff -r 5a57280b9125 -r f8a2f1fec8ef Analyse.xml
--- a/Analyse.xml	Thu Nov 10 07:34:57 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,92 +0,0 @@
-<tool id="LimmaAnalyse" name="Limma analysis" version="0.3.0">
-	<description>Perform gene expression analysis thanks to limma</description>
-	<requirements>
-	  	<container type="docker">sblanck/smagexp</container>
-	</requirements>
-	<command>
-		<![CDATA[ 
-		/galaxy-tools/stderr_wrapper.py Rscript
-		/galaxy-tools/transcriptomics/Analyse/Analyse.R
-		   	"${rdataset}"
-			"${conditions}"
-		 	"${selectCondition1}"
-			"${condition1}"
-		    "${selectCondition2}"
-			"${condition2}"
-			"${nbresult}"
-       		$result_export_eset
-       		$result_html 
-			$result_html.files_path
-			$result_tabular
-		/galaxy-tools/transcriptomics/Analyse/Analyse_tpl.html
-		]]>
-	</command>
-	
-	<inputs>
-		<param name="rdataset" type="data" format="rdata" label="RData" help="RData to be used"/>
-		<param name="conditions" type="data" format="cond" label="Conditions" help="conditions associated with the rData file"/>
-		<param name="selectCondition1" type="select" label="condition 1">
-			<options from_dataset="conditions">
-    		<column name="name" index="1"/>
-    		<column name="value" index="1"/>
-    		<filter type="unique_value" column="1"/>
-		</options>
-		</param>
-		<param name="condition1" type="select" display="checkboxes" label="Condition 1" multiple="true">
-			<options from_dataset="conditions">
-    		<column name="name" index="2"/>
-    		<column name="value" index="0"/>
-			<filter  type="param_value" ref="selectCondition1" column="1"/>
-		</options>
-		</param>	
-		<param name="selectCondition2" type="select" label="condition 2">
-			<options from_dataset="conditions">
-    		<column name="name" index="1"/>
-    		<column name="value" index="1"/>
-			<filter type="unique_value" column="1"/>    		
-		</options>
-		</param>	
-		<param name="condition2" type="select" display="checkboxes" label="Condition 2" multiple="true">
-			<options from_dataset="conditions">
-    		<column name="name" index="2"/>
-    		<column name="value" index="0"/>
-			<filter  type="param_value" ref="selectCondition2" column="1"/>
-		</options>
-		</param>	
-		<param name="nbresult" type="integer" value="1000" min="1" label="number of top genes" help="Number of genes to be displayed in result datatable"/>
-	</inputs>
-	<outputs>
-		<data format="html" name="result_html" label="Results of analysis of ${rdataset.name}"/>
-		<data format="rdata" name="result_export_eset" label="Export of expression set of ${rdataset.name}"/>
-		<data format="tabular" name="result_tabular" label="Text Results of analysis of ${rdataset.name}"/>
-		
-	</outputs>
-	<help>
-<![CDATA[ 
-**What it does**
-		
-The Limma analysis tool performs single analysis either of data previously retrieved from GEO database or normalized affymetrix .CEL files data. 
-Given a .cond file, it runs a standard limma differential expression analysis. 
-
-**Example** of .cond file      	
-
-The .cond file should look like this 
-::
-
- 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**
-		
-- Boxplots, p-value histograms and a volcano plot 
-- Table summarizing the differentially expressed genes and their annotations. This table is sortable and requestable.
-- Rdata object to perform further meta-analysis. 
-]]>
-	</help>
-
-</tool>
diff -r 5a57280b9125 -r f8a2f1fec8ef GEOQuery.xml
--- a/GEOQuery.xml	Thu Nov 10 07:34:57 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,65 +0,0 @@
-<tool id="GEOQuery" name="GEOQuery">
-	<description>GEOQuery wrapper</description>
-	<requirements>
-	  	<container type="docker">sblanck/smagexp</container>
-	</requirements>
-	<command>
-		<![CDATA[ 
-			/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>
-<![CDATA[ 
-**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>
diff -r 5a57280b9125 -r f8a2f1fec8ef ImportDataFromMatrix.xml
--- a/ImportDataFromMatrix.xml	Thu Nov 10 07:34:57 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,78 +0,0 @@
-<tool id="importMatrixData" name="Import custom data">
-	<description>Quality control and normalization of a custom matrix expression data</description>
-	<requirements>
-	  	<container type="docker">sblanck/smagexp</container>
-	</requirements>
-	<command>
-		<![CDATA[ 
-		/galaxy-tools/stderr_wrapper.py Rscript 
-		/galaxy-tools/transcriptomics/ImportDataFromMatrix/ImportDataFromMatrix.R
-		    $input
-			$normalization
-			$conditions
-			$annotations
-			$result_export_eset
-       		$result_html
-			$result_html.files_path
-		/galaxy-tools/transcriptomics/ImportDataFromMatrix/ImportDataFromMatrix_tpl.html
-		]]>		
-		</command>
-		
-	
-	<inputs>
-		<param name="input" type="data" format="tabular" label="Input data" help="Input data"/>
-		<param name="normalization" type="select" label="Preprocessing/normalization">
-    		<option value="quantile">quantile normalization + log2</option>
-            <option value="log2">log2 only</option>
-            <option value="none">none</option>
-		</param>
-		<param name="conditions" type="data" format="cond" label="Conditions" help="conditions associated with the input file"/>
-		<param name="annotations" type="text" label="Annotation GPL code" help="GPL code for annotations"/>		
-	</inputs>
-
-	<outputs>
-		<data format="rdata" name="result_export_eset" label="export normalized expressionSet"/>		
-		<data format="html" name="result_html" label="QC result"/>
-	</outputs>
-
-	<help>
-<![CDATA[ 
-**What it does**
-		     	
-This tool imports data stored in a tabular text file. 
-Column titles (chip IDs) must match the IDs of the .cond file.
-GPL annotation code is also required to fetch annotations from GEO.
-
-**Exemple**
-
-Header of input tabular text file
-::
-
-""	"GSM80460"	"GSM80461"	"GSM80462"	"GSM80463"	"GSM80464"
-"1007_s_at"	-0.0513991525066443	0.306845500314283	0.0854246562526777	-0.142417044615852	0.0854246562526777
-"1053_at"	-0.187707155126729	-0.488026018218199	-0.282789700980404	0.160920188181103	0.989865622866287
-"117_at"	0.814755482809874	-2.15842936260448	-0.125006361067033	-0.256700472111743	0.0114956388378294
-"121_at"	-0.0558912008920451	-0.0649174766813385	0.49467161164755	-0.0892673380970874	0.113700499164728
-"1294_at"	0.961993677420255	-0.0320936297098533	-0.169744675832317	-0.0969617298870879	-0.181149439104566
-"1316_at"	0.0454429707611671	0.43616183931445	-0.766111939825723	-0.182786075741673	0.599317793698226
-"1405_i_at"	2.23450132056221	0.369606070031838	-1.06190243892591	-0.190997225060914	0.595503660502742
-
-
-The .cond file should look like this 
-::
-
- 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**
-	- Bboxplots and MA plots 
-	- Rdata object containing the data for further analysis.
-]]>
-	</help>
-
-</tool>
\ No newline at end of file
diff -r 5a57280b9125 -r f8a2f1fec8ef MetaMA.xml
--- a/MetaMA.xml	Thu Nov 10 07:34:57 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,50 +0,0 @@
-<tool id="metaMA" name="Microarray data meta-analysis" version="0.1.0">
-	<description>Perform meta-analysis thanks to metaMA.</description>
-	<requirements>
-	  <container type="docker">sblanck/smagexp</container>
-	</requirements>
-	<command>
-		<![CDATA[ 
-		/galaxy-tools/stderr_wrapper.py Rscript 
-		/galaxy-tools/transcriptomics/MetaMA/MetaMA.R
-		#for $currentInput in $inputList
-        	"${currentInput.rdataset}"
-		 #end for
-       		$result_html 
-			$result_html.extra_files_path
-		/galaxy-tools/transcriptomics/MetaMA/MetaMa_tpl.html
-		]]>
-	</command>
-	
-	<inputs>
-		<repeat name="inputList" title="Datasets">
-			<param name="rdataset" type="data" format="rdata" label="RData" help="RData to be used"/>
-		</repeat>
-	</inputs>
-	
-	<outputs>
-		<data format="html" name="result_html" label="Meta-analysis results"/>
-	</outputs>
-
-	<help>
-<![CDATA[ 
-**What it does**
-		
-Given several Rdata object this tool run a meta-analysis using the metaMA R package.
-		
-**Results**
-		
-- Venn Diagram summarizing the results of the meta-analysis
-- A list of indicators to evaluate the quality of the performance of the meta-analysis
-		
-	- DE : Number of differentially expressed genes 
-	- IDD (Integration Driven discoveries) : number of genes that are declared differentially expressed in the meta-analysis that were not identified in any of the single studies alone
-	- Loss : Number of genes that are identified differentially expressed in single studies but not in meta-analysis 
-	- DR (Integration-driven Discovery Rate) : corresponding proportion of IDD
-	- IRR (Integration-driven Revision) : corresponding proportion of Loss
-		
-- Fully sortable and requestable table, with gene annotations and hypertext links to NCBI gene database.
-]]>
-	</help>
-
-</tool>
diff -r 5a57280b9125 -r f8a2f1fec8ef MetaRNAseq.xml
--- a/MetaRNAseq.xml	Thu Nov 10 07:34:57 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-<tool id="metarnaseq" name="RNA-seq data meta-analysis">
-	<description>perform meta-analysis thanks to metaRNAseq</description>
-	<requirements>
-	  	<container type="docker">sblanck/smagexp</container>
-	</requirements>
-	<command>
-		<![CDATA[ 	
-		/galaxy-tools/stderr_wrapper.py Rscript 
-		/galaxy-tools/transcriptomics/MetaRNASeq/MetaRNASeq.R 
-		#for $currentInput in $inputList
-        	"${currentInput}"
-			"${currentInput.name}"	
-		 #end for	
-			$top_table 
-			$diagnostic_html 
-			"$diagnostic_html.files_path"
-		/galaxy-tools/transcriptomics/MetaRNASeq/MetaRNASeq_tpl.html
-	]]>	
-	</command>
-
-	<inputs>
-		<param format="tabular" name="inputList" multiple="true" type="data" optional="false" label="Counts file" help="Must have the same number of row in each study. The experimental conditions must be specified in the header of each file"/>
-	</inputs>
-
-	<outputs>
-		<data format="tabular" name="top_table" label="Summary of meta-analysis and single studie analysis from ${tool.name} on ${on_string}"/>
-		<data format="html" name="diagnostic_html" label="Charts for ${tool.name} on ${on_string}"/>
-	</outputs>
-
-	<help>
-		
-	</help>
-
-</tool>
diff -r 5a57280b9125 -r f8a2f1fec8ef repository_dependencies.xml
--- a/repository_dependencies.xml	Thu Nov 10 07:34:57 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-<?xml version="1.0"?>
-<repositories description="smagexp datatypes">
-  <repository changeset_revision="f66f8566fd75" name="smagexp_datatypes" owner="sblanck" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-</repositories>