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Commit message:
Deleted selected files |
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ras_generator.xml |
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| diff -r 89047227bedc -r f8a1fafeaedf ras_generator.xml --- a/ras_generator.xml Wed Jan 22 11:45:41 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,172 +0,0 @@ -<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> - |