| Previous changeset 86:b6af3f72fd28 (2021-06-07) Next changeset 88:66432fdf1768 (2021-06-07) |
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Commit message:
Deleted selected files |
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removed:
Marea/ras_generator.xml ras_generator.xml |
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| diff -r b6af3f72fd28 -r 720e8301a90e Marea/ras_generator.xml --- a/Marea/ras_generator.xml Mon Jun 07 14:13:57 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,113 +0,0 @@ -<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> - |
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| diff -r b6af3f72fd28 -r 720e8301a90e ras_generator.xml --- a/ras_generator.xml Mon Jun 07 14:13:57 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,113 +0,0 @@ -<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> - |