marea: Marea/marea.xml comparison

comparison Marea/marea.xml @ 48:e4235b5231e4 draft

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author	bimib
date	Sun, 23 Feb 2020 09:41:14 -0500
parents	3af9d394367c
children	1c0cb543af19

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-:3af9d394367c
+:e4235b5231e4
-<tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.7">
+<tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.8">
 	<macros>
 		<import>marea_macros.xml</import>
 	</macros>
 	<requirements>
 		<requirement type="package" version="0.23.0">pandas</requirement>
 --names
 #for $data in $cond.input_Datasets:
 ${data.input_name}
 #end for
 --comparison ${cond.comparis.comparison}
+#if $cond.advanced.cond_map == 'true':
+	--custom_rules true
+	--custom_rule ${cond.advanced.cond_map.custom_rule}
+	--custom_map ${cond.advanced.cond_map.custom_map}
+#end if
 #if $cond.advanced.choice == 'true':
 	       --pValue ${cond.advanced.pValue}
 	       --fChange ${cond.advanced.fChange}
 	           --generate_svg ${cond.advanced.generateSvg}
 	    	   --generate_pdf ${cond.advanced.generatePdf}
 --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.cond_map == 'true':
+	--custom_rules true
+	--custom_rule ${cond.advanced.cond_map.custom_rule}
+	--custom_map ${cond.advanced.cond_map.custom_map}
 #end if
 #if $cond.advanced.choice == 'true':
 	        --pValue ${cond.advanced.pValue}
 	        --fChange ${cond.advanced.fChange}
 	            --generate_svg ${cond.advanced.generateSvg}
 						<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">
+						<param name="choice" type="boolean" checked="false" label="Use custom map and rules?" 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_rule" argument="--custom_rule" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
 							<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="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_rule" argument="--custom_rule" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
 							<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" />
 	<![CDATA[
 What it does
 -------------
-This tool analyzes RNA-seq dataset(s) as described in Graudenzi et al."`MaREA`_: Metabolic feature extraction, enrichment and visualization of RNAseq data" bioRxiv (2018): 248724.
+This tool analyzes and visualizes differences in the Reaction Activity Scores (RASs) of groups of samples, as computed by the Expression2RAS tool, of groups of samples.
 Accepted files are:
-- option 1) two or more RNA-seq datasets, each referring to samples in a given condition/class. The user can specify a label for each class (as e.g. "*classA*" and "*classB*");
+- option 1) two or more RAS datasets, each referring to samples in a given group. The user can specify a label for each group (as e.g. "classA" and "classB");
-- option 2) one RNA dataset and one class-file specifying the class/condition each sample belongs to.
+- option 2) one RAS dataset and one group-file specifying the group each sample belongs to.
+RAS datasets format: tab-separated text files, reporting the RAS value of each reaction (row) for a given sample (column).
+Column header: sample ID.
+Raw header: reaction ID.
 Optional files:
-- custom GPR (Gene-Protein-Reaction) rules. Two accepted formats:
-	* (Cobra Toolbox and CobraPy compliant) xml of metabolic model;
-	* .csv file specifyig for each reaction ID (column 1) the corresponding GPR rule (column 2).
 - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.
 The tool generates:
-1) a tab-separated file: reporting fold-change and p-values of reaction activity scores (RASs) between a pair of conditions/classes;
+- 1) a tab-separated file: reporting fold-change and p-values of reaction activity scores (RASs) between a pair of conditions/classes;
-2) a metabolic map file (downlodable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes;
+- 2) a metabolic map file (downloadable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes;
-3) a log file (.txt).
+- 3) a log file (.txt).
-RNA-seq datasets format: tab-separated text files, reporting the expression level (e.g., TPM, RPKM, ...) of each gene (row) for a given sample (column). Header: sample ID.
+Output options:
+To calculate P-Values and Fold-Changes and to enrich maps, comparisons are performed for each possible pair of groups (default option ‘One vs One’).
-Class-file format: each row of the class-file reports the sample ID (column1) and the label of the class/condition the sample belongs to (column 2).
+Alternative options are:
-To calculate P-Values and Fold-Changes and to generate maps, comparisons are performed for each possible pair of classes.
+- comparison of each group vs. the rest of samples (option ‘One vs Rest’)
+- comparison of each group vs. a control group (option ‘One vs Control). If this option is selected the user must indicate the control group label.
 Output files will be named as classA_vs_classB. Reactions will conventionally be reported as up-regulated (down-regulated) if they are significantly more (less) active in class having label "classA".
 Example input
 -------------
-**"Custom Rules"** option:
+"RAS of group 1 + RAS of group 2 + ... + RAS of group N" option:
-Custom Rules Dastaset:
+RAS Dataset 1:
-@CUSTOM_RULES_EXEMPLE@
++------------+----------------+----------------+----------------+
+| Reaction ID|   TCGAA62670   |   TCGAA62671   |   TCGAA62672   |
-**"RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N"** option:
++============+================+================+================+
+| r1642      |    0.523167    |    0.371355    |    0.925661    |
-RNA-seq Dataset 1:
++------------+----------------+----------------+----------------+
+| r1643      |    0.568765    |    0.765567    |    0.456789    |
-@DATASET_EXEMPLE1@
++------------+----------------+----------------+----------------+
+| r1640      |    0.876545    |    0.768933    |    0.987654    |
-RNA-seq Dataset 2:
++------------+----------------+----------------+----------------+
+| r1641      |    0.456788    |    0.876543    |    0.876542    |
-@DATASET_EXEMPLE2@
++------------+----------------+----------------+----------------+
+| r1646      |    0.876543    |    0.786543    |    0.897654    |
-**"RNAseq of all samples + sample group specification"** option:
++------------+----------------+----------------+----------------+
-RNA-seq Dataset:
+RAS Dataset 2:
-@DATASET_EXEMPLE1@
++------------+----------------+----------------+----------------+
+| Reaction ID|   TCGAA62670   |   TCGAA62671   |   TCGAA62672   |
-Class-file:
++============+================+================+================+
+| r1642      |    0.523167    |    0.371355    |    0.925661    |
-+------------+------------+
++------------+----------------+----------------+----------------+
-| Patient_ID |    class   |
+| r1643      |    0.568765    |    0.765567    |    0.456789    |
-+============+============+
++------------+----------------+----------------+----------------+
-| TCGAAA3529 |     MSI    |
+| r1640      |    0.876545    |    0.768933    |    0.987654    |
-+------------+------------+
++------------+----------------+----------------+----------------+
-| TCGAA62671 |     MSS    |
+| r1641      |    0.456788    |    0.876543    |    0.876542    |
-+------------+------------+
++------------+----------------+----------------+----------------+
-| TCGAA62672 |     MSI    |
+| r1646      |    0.876543    |    0.786543    |    0.897654    |
-+------------+------------+
++------------+----------------+----------------+----------------+
-|
+"RAS of all samples + sample group specification" option:
+RAS Dataset:
++------------+----------------+----------------+----------------+
+| Reaction ID|   TCGAA62670   |   TCGAA62671   |   TCGAA62672   |
++============+================+================+================+
+| r1642      |    0.523167    |    0.371355    |    0.925661    |
++------------+----------------+----------------+----------------+
+| r1643      |    0.568765    |    0.765567    |    0.456789    |
++------------+----------------+----------------+----------------+
+| r1640      |    0.876545    |    0.768933    |    0.987654    |
++------------+----------------+----------------+----------------+
+| r1641      |    0.456788    |    0.876543    |    0.876542    |
++------------+----------------+----------------+----------------+
+| r1646      |    0.876543    |    0.786543    |    0.897654    |
++------------+----------------+----------------+----------------+
+Group-file
++---------------+-----------+
+| Patient ID    |   Class   |
++===============+===========+
+| TCGAAA3529    |    MSI    |
++---------------+-----------+
+| TCGAA62671    |    MSS    |
++---------------+-----------+
+| TCGAA62672    |    MSI    |
++---------------+-----------+
+Advanced options
+----------------
+P-Value threshold: the threshold used for significance Kolmogorov-Smirnov (KS) test, to verify whether the distributions of RASs over the samples in two sets are significantly different
+Fold-Change threshold: threshold of the fold-change between the average RAS of two groups. Among the reactions that pass the KS test, only fold-change values larger than the indicated threshold will be visualized on the output metabolic map;
 .. class:: infomark
 **TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_.

Mercurial > repos > bimib > marea

comparison Marea/marea.xml @ 48:e4235b5231e4 draft