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ras_generator.xml |
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| diff -r 9acbdbc772f0 -r 035ba1736d38 ras_generator.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ras_generator.xml Mon Jun 07 14:12:52 2021 +0000 |
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| @@ -0,0 +1,113 @@ +<tool id="MaREA RAS Generator" name="Expression2RAS" version="1.0.7"> + <description>- Reaction Activity Scores computation</description> + <macros> + <import>marea_macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="0.25.3">pandas</requirement> + <requirement type="package" version="1.6.3">scipy</requirement> + <requirement type="package" version="4.6.3">lxml</requirement> + <requirement type="package" version="1.1.0">svglib</requirement> + <requirement type="package" version="3.5.67">reportlab</requirement> + </requirements> + <command detect_errors="exit_code"> + <![CDATA[ + python $__tool_directory__/ras_generator.py + --rules_selector $cond_rule.rules_selector + --input $input + --none $none + --tool_dir $__tool_directory__ + --out_log $log + --ras_output $ras_output + #if $cond_rule.rules_selector == 'Custom' + --custom $cond_rule.Custom_rules + #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" /> + </when> + </conditional> + <param name="input" argument="--input" type="data" format="tabular, csv, tsv" label="Gene Expression dataset:" /> + <param name="name" argument="--name" 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)?" /> + </inputs> + + <outputs> + <data format="txt" name="log" label="Expression2RAS - $name - Log" /> + <data format="tabular" name="ras_output" label="$name RAS"/> + </outputs> + + <help> +<![CDATA[ + +What it does +------------- + +This tool computes Reaction Activity Scores from gene expression (RNA-seq) dataset(s), as described in Graudenzi et al. Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power. Journal of Biomedical Informatics, 2018, 87: 37-49. + +Accepted files: + - A gene expression dataset + +Format: +Tab-separated text file reporting the normalized expression level (e.g., TPM, RPKM, ...) of each gene (row) for a given sample (column). +Column header: sample ID. +Row header: gene 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). + +Computation option ‘(A and NaN) solved as (A)’: +In case of missing expression value, referred to as NaN (Not a Number), for a gene joined with an AND operator in a given GPR rule, the rule ‘A and NaN’ + +If YES is selected: the GPR will be solved as A. + +If NO is selected: the GPR will be disregarded tout-court (i.e., treated as NaN). + +Example input +------------- + +Custom GPR rules: + ++------------+--------------------------------------+ +| id | rule (with entrez-id | ++============+======================================+ +| r1642 | 155060 or 10357 | ++------------+--------------------------------------+ +| r1643 | 155060 or 100134869 | ++------------+--------------------------------------+ +| r1640 | 155060 and 100134869 or 10357 | ++------------+--------------------------------------+ + +RNA-seq dataset: + ++------------+----------------+----------------+----------------+ +| Hugo_ID | TCGAA62670 | TCGAA62671 | TCGAA62672 | ++============+================+================+================+ +| HGNC:24086 | 0.523167 | 0.371355 | 0.925661 | ++------------+----------------+----------------+----------------+ +| HGNC:24086 | 0.568765 | 0.765567 | 0.456789 | ++------------+----------------+----------------+----------------+ +| HGNC:9876 | 0.876545 | 0.768933 | 0.987654 | ++------------+----------------+----------------+----------------+ +| HGNC:9 | 0.456788 | 0.876543 | 0.876542 | ++------------+----------------+----------------+----------------+ +| HGNC:23 | 0.876543 | 0.786543 | 0.897654 | ++------------+----------------+----------------+----------------+ + +]]> + </help> +<expand macro="citations" /> +</tool> + |