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Marea/ras_generator.xml |
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| diff -r f8a1fafeaedf -r 7aa966c488a4 Marea/ras_generator.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Marea/ras_generator.xml Wed Jan 22 11:46:11 2020 -0500 |
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| @@ -0,0 +1,172 @@ +<tool id="MaREA RAS Generator" name="RAS Generator" version="1.0.0"> + <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[ + python $__tool_directory__/marea.py + --rules_selector $cond_rule.rules_selector + --tool_dir $__tool_directory__ + --option $cond.type_selector + --out_log $log + --input_datas ${input_Datasets} + --single_ras_file $ras_single + --none ${cond.None} + #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="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> + </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"/> + </collection> + + </outputs> + <tests> + <test> + <param name="pValue" value="0.56"/> + <output name="log" file="log.txt"/> + </test> + </tests> + <help> +<![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. + +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. + +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). + +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. + +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: + +Custom Rules Dastaset: + +@CUSTOM_RULES_EXEMPLE@ + +**"RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N"** option: + +RNA-seq Dataset 1: + +@DATASET_EXEMPLE1@ + +RNA-seq Dataset 2: + +@DATASET_EXEMPLE2@ + +**"RNAseq of all samples + sample group specification"** option: + +RNA-seq Dataset: + +@DATASET_EXEMPLE1@ + +Class-file: + ++------------+------------+ +| Patient_ID | class | ++============+============+ +| TCGAAA3529 | MSI | ++------------+------------+ +| TCGAA62671 | MSS | ++------------+------------+ +| TCGAA62672 | MSI | ++------------+------------+ + +| + +.. class:: infomark + +**TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_. + +.. class:: infomark + +**TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_. + +@REFERENCE@ + +.. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724 +.. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj +.. _MaREA cluster analysis: http://link del tool di cluster.org + +]]> + </help> + <expand macro="citations" /> +</tool> + |