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changeset 0:27ffdb495852 draft default tip

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Imported from capsule None
author sblanck
date Wed, 13 Apr 2016 07:40:02 -0400
parents
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files AffyQCnormalization.xml CustomAnalyse.xml GEOAnalyse.xml GEOQuery.xml MetaMA.xml MetaRNAseq.xml repository_dependencies.xml
diffstat 7 files changed, 279 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/AffyQCnormalization.xml	Wed Apr 13 07:40:02 2016 -0400
@@ -0,0 +1,44 @@
+<tool id="QCnormalization" name="QCnormalization" version="0.1.0">
+	<description>Quality control and normalization of affymetric expression data</description>
+	<requirements>
+	  <container type="docker">sblanck/testtool:latest</container>
+	</requirements>
+	<command>
+
+		/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 expressionSet"/>		
+		<data format="html" name="result_html" label="QC result"/>
+	</outputs>
+
+	<help>
+	</help>
+
+</tool>
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CustomAnalyse.xml	Wed Apr 13 07:40:02 2016 -0400
@@ -0,0 +1,64 @@
+<tool id="customAnalyse" name="CustomAnalyse" version="0.1.0">
+	<description>Custom Analyse</description>
+	<requirements>
+	  <container type="docker">sblanck/testtool:latest</container>
+	</requirements>
+	<command>
+
+		/galaxy-tools/stderr_wrapper.py Rscript 
+		/galaxy-tools/transcriptomics/CustomAnalyse/CustomAnalyse.R
+		   	#for $input in $inputs
+                "${input}"
+			    "${input.name}"
+     		#end for
+			"${target}"
+			"${selectCondition1}"
+			"${selectCondition2}"
+			$result_export_eset
+       		$result_export_conditions
+			$result_html 
+			$result_html.files_path
+		/galaxy-tools/transcriptomics/CustomAnalyse/CustomAnalyse_tpl.html
+	</command>
+	
+	<inputs>
+	
+		<param name="inputs" type="data" format="cel" multiple="true" label=".CEL files" help=".CEL files to be used"/>
+
+		<param name="target" type="data" format="txt" label="target file" help="target file associated with the .CEL file dataset"/>
+		
+		<!--param name="normalisation" type="select" label="Preprocessing/normalization">
+		<options>
+    		<option value="rma">rma</option>
+            <option value="quantile">quantile normalization</option>
+            <option value="log2">log2</option>
+            <option value="none">none</option>
+		</options>	
+		</param-->
+				
+		<param name="selectCondition1" type="select" display="checkboxes" label="Condition 1" multiple="true">
+			<options from_dataset="target">
+    		<column name="name" index="0"/>
+    		<column name="value" index="0"/>
+		</options>
+		</param>	
+		
+		<param name="selectCondition2" type="select" display="checkboxes" label="Condition 2" multiple="true">
+			<options from_dataset="target">
+    		<column name="name" index="0"/>
+    		<column name="value" index="0"/>
+		</options>
+		</param>	
+	
+	</inputs>
+	<outputs>
+		<data format="html" name="result_html" label="Annotations"/>
+		<data format="rdata" name="result_export_eset" label="export expressionSet"/>		
+		<data format="cond" name="result_export_conditions" label="export conditions"/>
+	</outputs>
+
+	<help>
+		NOTE: This wrapper performs p-value combination from multiples studies with the same probes. If you need to normalize your data, use "matrix_normalisation" tool on each file. Then, use "Merge Standard datasets(copied)" tool to make a multiple file dataset.
+	</help>
+
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEOAnalyse.xml	Wed Apr 13 07:40:02 2016 -0400
@@ -0,0 +1,41 @@
+<tool id="metaMAGEOQuery" name="GEOanalyse" version="0.1.0">
+	<description>GEOAnalyse wrapper</description>
+	<requirements>
+	  <container type="docker">sblanck/testtool:latest</container>
+	</requirements>
+	<command>
+
+		/galaxy-tools/stderr_wrapper.py Rscript 
+		/galaxy-tools/transcriptomics/GEOanalyse/GEOAnalyse.R
+		   	"${rdataset}"
+		 	"${selectCondition}"
+       		$result_html 
+			$result_html.files_path
+		/galaxy-tools/transcriptomics/GEOanalyse/GEOAnalyse_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="selectCondition" type="select" label="case condition">
+			<options from_dataset="conditions">
+    		<column name="name" index="0"/>
+    		<column name="value" index="0"/>
+		</options>
+		</param>	
+	
+	</inputs>
+	<outputs>
+		<data format="html" name="result_html" label="Annotations"/>
+		
+	</outputs>
+
+	<help>
+		NOTE: This metaMA wrapper performs p-value combination from multiples studies with the same probes. If you need to normalize your data, use "matrix_normalisation" tool on each file. Then, use "Merge Standard datasets(copied)" tool to make a multiple file dataset.
+	</help>
+
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEOQuery.xml	Wed Apr 13 07:40:02 2016 -0400
@@ -0,0 +1,27 @@
+<tool id="GEOQuery" name="GEOQuery">
+	<description>GEOQuery wrapper</description>
+	<requirements>
+	  <container type="docker">sblanck/testtool:latest</container>
+	</requirements>
+	<command>
+		/galaxy-tools/stderr_wrapper.py Rscript /galaxy-tools/transcriptomics/GEOquery/GEOQuery.R $GEOQueryID $GEOQueryData $GEOQueryRData $conditions
+	</command>
+
+	<inputs>
+		<param name="GEOQueryID" type="text" size="12" optional="false" label="GEOQuery ID" help="">
+			<validator type="empty_field"/>
+		</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>
+		
+	</help>
+
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MetaMA.xml	Wed Apr 13 07:40:02 2016 -0400
@@ -0,0 +1,46 @@
+<tool id="metaMA" name="MetaMA" version="0.1.0">
+	<description>metaMA wrapper</description>
+	<requirements>
+	  <container type="docker">sblanck/testtool:latest</container>
+	</requirements>
+	<command>
+
+		/galaxy-tools/stderr_wrapper.py Rscript 
+		/galaxy-tools/transcriptomics/MetaMA/MetaMA.R
+		#for $currentInput in $inputList
+        	"${currentInput.rdataset}"
+		 	"${currentInput.selectCondition}"
+        #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"/>
+
+		<param name="conditions" type="data" format="cond" label="Conditions" help="conditions associated with the rData file"/>
+				
+		<param name="selectCondition" type="select" label="tumor condition">
+			<options from_dataset="conditions">
+    		<column name="name" index="0"/>
+    		<column name="value" index="0"/>
+		</options>
+		</param>	
+		
+	
+	
+	</repeat>
+	
+	</inputs>
+	<outputs>
+		<data format="html" name="result_html" label="Annotations"/>
+	    </outputs>
+
+	<help>
+		NOTE: This metaMA wrapper performs p-value combination from multiples studies with the same probes. If you need to normalize your data, use "matrix_normalisation" tool on each file. Then, use "Merge Standard datasets(copied)" tool to make a multiple file dataset.
+	</help>
+
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MetaRNAseq.xml	Wed Apr 13 07:40:02 2016 -0400
@@ -0,0 +1,53 @@
+<tool id="metarnaseq" name="metaRNASeq">
+	<description>metaRNASeq wrapper</description>
+	<requirements>
+	  <container type="docker">sblanck/testtool:latest</container>
+	</requirements>
+	<command>
+
+		/galaxy-tools/stderr_wrapper.py Rscript 
+		/galaxy-tools/transcriptomics/MetaRNASeq/MetaRNASeq.R 
+		#for $currentInput in $inputList
+        	"${currentInput}"
+			"${currentInput.name}"	
+		 #end for	
+			$comparison 
+			$method 
+			$mod 
+			$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"/>
+
+		<param name="method" type="select" label="Compute dispersion method" help="">
+			<option value="pooled">Pooled</option>
+			<option value="pooled-CR">Pooled-CR</option>
+			<option value="per-condition">Per-condition</option>
+			<option value="blind">Blind</option>
+		</param>
+		<param name="mod" type="select" label="Compute dispersion sharingmod" help="">
+			<option value="maximum">Maximum</option>
+			<option value="fit-only">Fit-only</option>
+			<option value="gene-est-only">Gene-est-only</option>
+		</param>
+
+		<param name="comparison" type="text" size="30" optional="false" label="Comparison type" help="A comma separated tuple (no spaces) of the comparison you want to do.  Must use the names from the Column Types list.  E.g. comparing kidney to liver: kidney,liver.  Comparing liver to kidney: liver,kidney">
+			<validator type="empty_field"/>
+			<validator type="regex" message="Must be a comma-separated tuple with no spaces">^\w+,\w+$</validator>
+		</param>
+	</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>
+		NOTE: This metaRNASeq Galaxy tool can only be run on counts files. 
+	</help>
+
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Wed Apr 13 07:40:02 2016 -0400
@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories description="MetaMA datatypes">
+  <repository changeset_revision="d54c187fecd9" name="meta_ma_datatypes" owner="sblanck" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+</repositories>