Mercurial > repos > bimib > marea
diff 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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--- a/Marea/marea.xml Wed Feb 19 10:44:52 2020 -0500 +++ b/Marea/marea.xml Sun Feb 23 09:41:14 2020 -0500 @@ -1,4 +1,4 @@ -<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> @@ -28,6 +28,11 @@ ${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} @@ -47,6 +52,11 @@ #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} @@ -90,11 +100,12 @@ <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"> + <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> @@ -131,6 +142,7 @@ <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> @@ -155,71 +167,108 @@ 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 2) one RNA dataset and one class-file specifying the class/condition each sample belongs to. + - 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 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; - 2) a metabolic map file (downlodable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes; - 3) a log file (.txt). + - 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 (downloadable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes; + - 3) a log file (.txt). + +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’). -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. - -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). - -To calculate P-Values and Fold-Changes and to generate maps, comparisons are performed for each possible pair of classes. +Alternative options are: + - 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@ - -**"RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N"** option: ++------------+----------------+----------------+----------------+ +| 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 | ++------------+----------------+----------------+----------------+ -RNA-seq Dataset 1: - -@DATASET_EXEMPLE1@ +RAS Dataset 2: -RNA-seq Dataset 2: ++------------+----------------+----------------+----------------+ +| 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 | ++------------+----------------+----------------+----------------+ -@DATASET_EXEMPLE2@ - -**"RNAseq of all samples + sample group specification"** option: +"RAS of all samples + sample group specification" option: -RNA-seq Dataset: +RAS Dataset: -@DATASET_EXEMPLE1@ ++------------+----------------+----------------+----------------+ +| 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 | ++------------+----------------+----------------+----------------+ -Class-file: +Group-file -+------------+------------+ -| Patient_ID | class | -+============+============+ -| TCGAAA3529 | MSI | -+------------+------------+ -| TCGAA62671 | MSS | -+------------+------------+ -| TCGAA62672 | MSI | -+------------+------------+ ++---------------+-----------+ +| 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