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diff Marea/marea.xml @ 47:3af9d394367c draft

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author bimib
date Wed, 19 Feb 2020 10:44:52 -0500
parents 7b1971251c63
children e4235b5231e4
line wrap: on
line diff
--- a/Marea/marea.xml	Wed Jan 22 11:50:54 2020 -0500
+++ b/Marea/marea.xml	Wed Feb 19 10:44:52 2020 -0500
@@ -1,28 +1,19 @@
-<tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.6">
-    <description></description>
-    <macros>
-        <import>marea_macros.xml</import>
-    </macros>
-    <requirements>
-        <requirement type="package" version="0.23.0">pandas</requirement>
-        <requirement type="package" version="1.1.0">scipy</requirement>
-        <requirement type="package" version="0.10.1">cobra</requirement>
-        <requirement type="package" version="4.2.1">lxml</requirement>
-        <requirement type="package" version="0.8.1">svglib</requirement>
-        <requirement type="package" version="3.4.0">reportlab</requirement>
-    </requirements>
-    <command detect_errors="exit_code">
-        <![CDATA[
+<tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.7">
+	<macros>
+		<import>marea_macros.xml</import>
+	</macros>
+	<requirements>
+		<requirement type="package" version="0.23.0">pandas</requirement>
+		<requirement type="package" version="1.1.0">scipy</requirement>
+		<requirement type="package" version="0.10.1">cobra</requirement>
+		<requirement type="package" version="4.2.1">lxml</requirement>
+		<requirement type="package" version="0.8.1">svglib</requirement>
+		<requirement type="package" version="3.4.0">reportlab</requirement>
+	</requirements>
+	<command detect_errors="exit_code">
+		<![CDATA[
       	python $__tool_directory__/marea.py
-        --rules_selector $cond_rule.rules_selector
-        #if $cond_rule.rules_selector == 'Custom':
-            --custom ${cond_rule.Custom_rules}
-            --yes_no ${cond_rule.cond_map.yes_no}
-            #if $cond_rule.cond_map.yes_no == 'yes':
-                --custom_map $cond_rule.cond_map.Custom_map
-            #end if
-        #end if
-	
+
       	--tool_dir $__tool_directory__
       	--option $cond.type_selector
         --out_log $log		
@@ -36,153 +27,130 @@
             #for $data in $cond.input_Datasets:
                 ${data.input_name}
             #end for
+            --comparison ${cond.comparis.comparison}
             #if $cond.advanced.choice == 'true':
-      	    --none ${cond.advanced.None}
-      	    --pValue ${cond.advanced.pValue}
-      	    --fChange ${cond.advanced.fChange}
-	    	--generate_svg ${cond.advanced.generateSvg}
-	    	--generate_pdf ${cond.advanced.generatePdf}
-	    --generate_ras ${cond.advanced.generateRas}
-	#else 
-	    --none true
-	    --pValue 0.05
-	    --fChange 1.5
-	    --generate_svg false
-	    --generate_pdf true
-	    --generate_ras false
-	#end if
+      	       --pValue ${cond.advanced.pValue}
+      	       --fChange ${cond.advanced.fChange}
+	           --generate_svg ${cond.advanced.generateSvg}
+	    	   --generate_pdf ${cond.advanced.generatePdf}
+     	    #else 
+	            --pValue 0.05
+	            --fChange 1.5
+	            --generate_svg false
+	            --generate_pdf true
+	            --generate_ras false
+	        #end if
         #elif $cond.type_selector == 'dataset_class':
             --input_data ${input_data}
             --input_class ${input_class}
+            --comparison ${cond.comparis.comparison}
+            #if $cond.comparis.comparison == 'onevsmany'
+            	--control ${cond.comparis.controlgroup}
+            #end if
             #if $cond.advanced.choice == 'true':
-      	    --none ${cond.advanced.None}
-      	    --pValue ${cond.advanced.pValue}
-      	    --fChange ${cond.advanced.fChange}
-	    --generate_svg ${cond.advanced.generateSvg}
-	    --generate_pdf ${cond.advanced.generatePdf}
-	    --generate_ras ${cond.advanced.generateRas}
-	#else 
-	    --none true
-	    --pValue 0.05
-	    --fChange 1.5
-	    --generate_svg false
-	    --generate_pdf true
-	    --generate_ras false
-	#end if
-        #end if
-        #if $cond.type_selector == 'datasets_rasonly':
-            --input_datas ${input_Datasets}
-            --single_ras_file $ras_single
-            --none ${cond.None}
+      	        --pValue ${cond.advanced.pValue}
+      	        --fChange ${cond.advanced.fChange}
+	            --generate_svg ${cond.advanced.generateSvg}
+	            --generate_pdf ${cond.advanced.generatePdf}
+	        #else 
+	            --pValue 0.05
+	            --fChange 1.5
+	            --generate_svg false
+	            --generate_pdf true
+	        #end if
         #end if
         ]]>
-    </command>
-
-    <inputs>
-        <conditional name="cond_rule">
-            <expand macro="options"/>
-            <when value="HMRcore">
-            </when>
-            <when value="Recon">
-            </when>
-            <when value="Custom">
-                <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
-                <conditional name="cond_map">
-                    <param name="yes_no" type="select" label="Custom map? (optional)">
-                        <option value="no" selected="true">no</option>
-                        <option value="yes">yes</option>
-                    </param>
-                    <when value="yes">
-                        <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
-                    </when>
-                    <when value="no">
-                    </when>
-                </conditional>
-            </when>
-        </conditional>
-        <conditional name="cond">
-            <param name="type_selector" argument="--option" type="select" label="Input format:">
-                <option value="datasets" selected="true">RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N</option>
-                <option value="dataset_class">RNAseq of all samples + sample group specification</option>
-                <option value="datasets_rasonly" selected="true">RNAseq dataset</option>
-            </param>
-            <when value="datasets">
-                <repeat name="input_Datasets" title="RNAseq" min="2">
-                    <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />	
-                    <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
-                </repeat>
-                <conditional name="advanced">
+	</command>
+	<inputs>
+		<conditional name="cond">
+			<param name="type_selector" argument="--option" type="select" label="Input format:">
+				<option value="datasets" selected="true">RAS of group 1 + RAS of group 2 + ... + RAS of group N</option>
+				<option value="dataset_class">RAS of all samples + sample group specification</option>
+			</param>
+			<when value="datasets">
+				<repeat name="input_Datasets" title="RAS dataset" min="2">
+					<param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
+					<param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
+				</repeat>
+				<conditional name="comparis">
+					<param name="comparison" argument="--comparison" type="select" label="Groups comparison:">
+						<option value="manyvsmany" selected="true">One vs One</option>
+						<option value="onevsrest">One vs All</option>
+						<option value="onevsmany">One vs Control</option>
+					</param>
+					<when value="onevsmany">
+						<param name="controlgroup" argument="--controlgroup" type="text" label="Control group label:" value="0" help="Name of group label to be compared to others"/>
+					</when>
+				</conditional>
+				<conditional name="advanced">
 					<param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom parameters for evaluation: pValue, Fold-Change threshold, how to solve (A and NaN) and specify output maps.">
-		    			<option value="true" selected="true">No</option>
-		    			<option value="false">Yes</option>
+						<option value="true" selected="true">No</option>
+						<option value="false">Yes</option>
 					</param>
-					<when value="false">
-					</when>
+					<when value="false"></when>
 					<when value="true">
-		    			<param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> 
-		    			<param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" />
-		    			<param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" />
-		    			<param name="generateSvg" argument="--generateSvg" type="boolean" checked="false" label="Generate SVG map" help="should the program generate an editable svg map of the processes?" />
-		    			<param name="generatePdf" argument="--generatePdf" type="boolean" checked="true" label="Generate PDF map" help="should the program return a non editable (but displayble) pdf map of the processes?" />	
-		    			<param name="generateRas" argument="--generateRas" type="boolean" checked="false" label="Generate Reaction Activity Score for each table" help="Generate Reaction Activity Score for each table" />		
+						<conditional name="cond_map">
+						<param name="choice" type="boolean" checked="false" label="Use custom map?" help="Use this option only if you have generated RAS using a custom set of rules">
+							<option value="false" selected="true">No</option>
+							<option value="true">Yes</option>
+						</param>
+						<when value="true">							
+							<param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
+						</when>
+					</conditional>
+						<param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" />
+						<param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" />
+						<param name="generateSvg" argument="--generateSvg" type="boolean" checked="false" label="Generate SVG map" help="should the program generate an editable svg map of the processes?" />
+						<param name="generatePdf" argument="--generatePdf" type="boolean" checked="true" label="Generate PDF map" help="should the program return a non editable (but displayble) pdf map of the processes?" />
 					</when>
-    	</conditional>
-            </when>
-            <when value="datasets_rasonly">
-                <param name="input_Datasets" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
-                <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
-                <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> 
-            </when>
-            <when value="dataset_class">
-                <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" />
+			</conditional>
+			</when>
+			<when value="dataset_class">
+                <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RAS of all samples" />
                 <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" />
-                <conditional name="advanced">
-					<param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom parameters for evaluation: pValue, Fold-Change threshold, how to solve (A and NaN) and specify output maps.">
-		    			<option value="true" selected="true">No</option>
-		    			<option value="false">Yes</option>
+                <conditional name="comparis">
+					<param name="comparison" argument="--comparison" type="select" label="Groups comparison:">
+						<option value="manyvsmany" selected="true">One vs One</option>
+						<option value="onevsrest">One vs All</option>
+						<option value="onevsmany">One vs Control</option>
 					</param>
-					<when value="false">
-					</when>
-					<when value="true">
-		    			<param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> 
-		    			<param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" />
-		    			<param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" />
-		    			<param name="generateSvg" argument="--generateSvg" type="boolean" checked="false" label="Generate SVG map" help="should the program generate an editable svg map of the processes?" />
-		    			<param name="generatePdf" argument="--generatePdf" type="boolean" checked="true" label="Generate PDF map" help="should the program return a non editable (but displayble) pdf map of the processes?" />	
-		    			<param name="generateRas" argument="--generateRas" type="boolean" checked="false" label="Generate Reaction Activity Score for each table" help="Generate Reaction Activity Score for each table" />		
+					<when value="onevsmany">
+						<param name="controlgroup" argument="--controlgroup" type="text" label="Control group label:" value="0" help="Name of group label to be compared to others"/>
 					</when>
-    	</conditional>
-            </when>
-        </conditional>
-       
-      
-       
-	
-    </inputs>
-
-    <outputs>
-        <data format="txt" name="log" label="MaREA - Log" />
-        <data format="tabular" name="ras_single" label="MaREA - RAS - ${cond.input_name}">
-        	<filter>cond['type_selector'] == "datasets_rasonly"</filter>
-        </data>
-        <collection name="results" type="list" label="MaREA - Results">
-        <filter>cond['type_selector'] == "datasets" or cond['type_selector'] == "dataset_class"</filter>
-            <discover_datasets pattern="__name_and_ext__" directory="result"/>
-        </collection>
-	<collection name="ras" type="list" label="MaREA - RAS list" format_source="tabular">
-	    <filter>cond['type_selector'] != "datasets_rasonly" and cond['advanced']['choice'] and cond['advanced']['generateRas']</filter>
-    	    <discover_datasets pattern="__name_and_ext__" directory="ras" format="tabular"/>
+				</conditional>
+				<conditional name="advanced">
+				<param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom parameters for evaluation: pValue, Fold-Change threshold, how to solve (A and NaN) and specify output maps.">
+					<option value="true" selected="true">No</option>
+					<option value="false">Yes</option>
+				</param>
+				<when value="false"></when>
+				<when value="true">
+					<conditional name="cond_map">
+						<param name="choice" type="boolean" checked="false" label="Use custom map?" help="Use this option only if you have generated RAS using a custom set of rules">
+							<option value="false" selected="true">No</option>
+							<option value="true">Yes</option>
+						</param>
+						<when value="true">							
+							<param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
+						</when>
+					</conditional>
+					<param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" />
+					<param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" />
+					<param name="generateSvg" argument="--generateSvg" type="boolean" checked="false" label="Generate SVG map" help="should the program generate an editable svg map of the processes?" />
+					<param name="generatePdf" argument="--generatePdf" type="boolean" checked="true" label="Generate PDF map" help="should the program return a non editable (but displayble) pdf map of the processes?" />
+				</when>
+			</conditional>
+		</when>
+	</conditional>
+</inputs>
+<outputs>
+	<data format="txt" name="log" label="MaREA - Log" />
+	<collection name="results" type="list" label="MaREA - Results">
+		<discover_datasets pattern="__name_and_ext__" directory="result"/>
 	</collection>
-	
-    </outputs>
-    <tests>
-        <test>
-            <param name="pValue" value="0.56"/>
-            <output name="log" file="log.txt"/>
-        </test>
-    </tests>
-    <help>
-<![CDATA[
+</outputs>
+<help>
+	<![CDATA[
 
 What it does
 -------------
@@ -268,7 +236,6 @@
 .. _MaREA cluster analysis: http://link del tool di cluster.org
 
 ]]>
-    </help>
-    <expand macro="citations" />
-</tool>
+</help>
+<expand macro="citations" />undefined</tool>