Mercurial > repos > bimib > cobraxy
changeset 561:a1835dea4686 draft default tip
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--- a/COBRAxy/src/marea.py Fri Feb 06 15:30:54 2026 +0000 +++ b/COBRAxy/src/marea.py Fri Feb 06 15:33:57 2026 +0000 @@ -1017,21 +1017,12 @@ """ global ARGS ARGS = process_args(args) - - print(ARGS.upRegCol) - print(ARGS.downRegCol) - - print(ArrowColor.UpRegulated) - print(ArrowColor.DownRegulated) - + ArrowColor.updateColors( UpRegulated=ARGS.upRegCol, DownRegulated=ARGS.downRegCol, ) - print(ArrowColor.UpRegulated) - print(ArrowColor.DownRegulated) - # Create output folder if not os.path.isdir(ARGS.output_path): os.makedirs(ARGS.output_path, exist_ok=True)
--- a/COBRAxy/src/marea.xml Fri Feb 06 15:30:54 2026 +0000 +++ b/COBRAxy/src/marea.xml Fri Feb 06 15:33:57 2026 +0000 @@ -200,8 +200,8 @@ <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" /> <param name="generateSvg" argument="--generateSvg" type="boolean" checked="false" label="Generate SVG map" help="should the program generate an editable svg map of the processes?" /> <param name="generatePdf" argument="--generatePdf" type="boolean" checked="true" label="Generate PDF map" help="should the program return a non editable (but displayble) pdf map of the processes?" /> - <param name="upRegCol" argument="--upRegCol" type="text" label="Up-regulated color" value="#ecac68" help="Color for up-regulated reactions " /> - <param name="downRegCol" argument="--downRegCol" type="text" label="Down-regulated color" value="#6495ed" help="Color for down-regulated reactions " /> + <param name="upRegCol" argument="--upRegCol" type="text" label="Up-regulated color" value="ecac68" help="Color for up-regulated reactions " /> + <param name="downRegCol" argument="--downRegCol" type="text" label="Down-regulated color" value="6495ed" help="Color for down-regulated reactions " /> <param name="netRPS" argument="--net" type="boolean" checked="false" label="Should RPS enrichment use net values?" help="If checked and RPS datasets are present the arrow tips of a reversible arrow will be colored with the net contribution of both directions' RPS values" /> </when>
--- a/marea.xml Fri Feb 06 15:30:54 2026 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,352 +0,0 @@ -<tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="2.0.0"> - <macros> - <import>marea_macros.xml</import> - </macros> - - <requirements> - <requirement type="package" version="1.24.4">numpy</requirement> - <requirement type="package" version="2.0.3">pandas</requirement> - <requirement type="package" version="5.2.2">lxml</requirement> - <requirement type="package" version="1.11">scipy</requirement> - <requirement type="package" version="1.5.1">svglib</requirement> - <requirement type="package" version="2.2.3">pyvips</requirement> - <requirement type="package" version="2.7.1">cairosvg</requirement> - <requirement type="package" version="0.29.0">cobra</requirement> - <requirement type="package" version="0.8.0">anndata</requirement> - <requirement type="package" version="1.11">scipy</requirement> - <requirement type="package" version="1.3.2">scikit-learn</requirement> - <requirement type="package" version="0.5.1">pydeseq2</requirement> - </requirements> - - <command detect_errors="exit_code"> - <![CDATA[ - python $__tool_directory__/marea.py - - --tool_dir $__tool_directory__ - --option $cond.type_selector - --out_log $log - - #if $cond.type_selector == 'datasets': - - --using_RAS $cond.using_ras.check - --using_RPS $cond.using_rps.check - - #if $cond.using_ras.check == 'true': - --input_datas - #for $data in $cond.using_ras.input_datasets: - ${data.input} - #end for - - --names - #for $data in $cond.using_ras.input_datasets: - ${data.input_name} - #end for - #end if - - #if $cond.using_rps.check == 'true': - --input_datas_rps - #for $data in $cond.using_rps.input_datasets_rps: - ${data.input_rps} - #end for - - --names_rps - #for $data in $cond.using_rps.input_datasets_rps: - ${data.input_name_rps} - #end for - #end if - - #elif $cond.type_selector == 'dataset_class': - - --using_RAS $cond.using_ras_all.check - --using_RPS $cond.using_rps_all.check - - #if $cond.using_ras_all.check == 'true': - --input_data ${cond.using_ras_all.input_data} - --input_class ${cond.using_ras_all.input_class} - #end if - - #if $cond.using_rps_all.check == 'true': - --input_data_rps ${cond.using_rps_all.input_data_rps} - --input_class_rps ${cond.using_rps_all.input_class_rps} - #end if - #end if - - --comparison ${comparis.comparison} - #if $comparis.comparison == 'onevsmany' - --control '${comparis.controlgroup}' - #end if - - --choice_map '${cond_choice_map.choice_map}' - #if $cond_choice_map.choice_map == 'Custom': - --custom_map ${cond_choice_map.custom_map} - #end if - - #if $advanced.choice == 'true': - --test ${advanced.test} - --pValue ${advanced.pValue} - --adjusted ${advanced.adjusted} - --fChange ${advanced.fChange} - --generate_svg ${advanced.generateSvg} - --generate_pdf ${advanced.generatePdf} - --net ${advanced.netRPS} - --upRegCol '#${advanced.upRegCol}' - --downRegCol '#${advanced.downRegCol}' - #else - --test 'ks' - --pValue 0.05 - --adjusted false - --fChange 1.2 - --generate_svg false - --generate_pdf true - --net false - --upRegCol '#ecac68' - --downRegCol '#6495ed' - #end if - ]]> - </command> - - <inputs> - <conditional name="cond"> - <param name="type_selector" argument="--option" type="select" label="Input format:"> - <option value="datasets" selected="true">RAS of group 1 + RAS of group 2 + ... + RAS of group N</option> - <option value="dataset_class">RAS of all samples + sample group specification</option> - </param> - - <when value="datasets"> - <conditional name = "using_ras"> - <param name = "check" argument = "--using_ras" type = "boolean" checked = "true" label = "Using RAS datasets." /> - - <when value = "true"> - <repeat name="input_datasets" title="RAS dataset" min="2"> - <param name="input" 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" /> - </repeat> - </when> - </conditional> - - <conditional name = "using_rps"> - <param name = "check" argument = "--using_rps" type = "boolean" checked = "false" label = "Using RPS datasets." /> - - <when value = "true"> - <repeat name="input_datasets_rps" title="RPS dataset" min="2"> - <param name="input_rps" argument="--input_datas_rps" type="data" format="tabular, csv, tsv" label="add dataset" /> - <param name="input_name_rps" argument="--names_rps" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" /> - </repeat> - </when> - </conditional> - </when> - - <when value="dataset_class"> - <conditional name = "using_ras_all"> - <param name = "check" argument = "--using_ras_all" type = "boolean" checked = "true" label = "Using RAS datasets." /> - - <when value = "true"> - <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RAS of all samples" /> - <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" /> - </when> - </conditional> - - <conditional name = "using_rps_all"> - <param name = "check" argument = "--using_rps_all" type = "boolean" checked = "false" label = "Using RPS datasets." /> - - <when value = "true"> - <param name="input_data_rps" argument="--input_data_rps" type="data" format="tabular, csv, tsv" label="RPS of all samples" /> - <param name="input_class_rps" argument="--input_class_rps" type="data" format="tabular, csv, tsv" label="Sample group specification" /> - </when> - </conditional> - </when> - </conditional> - - <conditional name="comparis"> - <param name="comparison" argument="--comparison" type="select" label="Groups comparison:"> - <option value="manyvsmany" selected="true">One vs One</option> - <option value="onevsrest">One vs All</option> - <option value="onevsmany">One vs Control</option> - </param> - <when value="onevsmany"> - <param name="controlgroup" argument="--controlgroup" type="text" label="Control group label:" value="0" help="Name of group label to be compared to others"/> - </when> - </conditional> - - <conditional name="cond_choice_map"> - <param name="choice_map" argument="--choice_map" type="select" label="Choose metabolic map:"> - <option value="ENGRO2" selected="true">ENGRO2</option> - <option value="HMRcore">HMRcore</option> - <option value="Custom">Custom</option> - </param> - - <when value="Custom"> - <param name="custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/> - </when> - </conditional> - - <conditional name="advanced"> - <param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom parameters for evaluation: statistical test, pValue, Fold-Change threshold, how to solve (A and NaN) and specify output maps."> - <option value="true" selected="true">No</option> - <option value="false">Yes</option> - </param> - - <when value="true"> - <param name="test" argument="--test" type="select" label="Statistical test to use:" help="Select the statistical test to use for the analysis based on your data and the amount of replicates. Paired T-test and Wilcoxon need the same number of replicates in each group."> - <option value="ks" selected="true">Kolmogorov-Smirnov</option> - <option value="ttest_p">T-test (paired)</option> - <option value="ttest_ind">T-test (unpaired)</option> - <option value="wilcoxon">Wilcoxon</option> - <option value="mw">Mann-Whitney</option> - <option value="DESeq">DESeq2-like statistical test (requires at least 2 replicates per sample, to use ONLY with RAS)</option> - </param> - <param name="pValue" argument="--pValue" type="float" size="20" value="0.05" max="1" min="0" label="P-value threshold:" help="min value 0" /> - <param name="adjusted" argument="--adjusted" type="boolean" checked="false" label="Use adjusted p-values" help="Should the program adjust the P-values based on the FDR (Benjamini-Hochberg) correction?" /> - <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" /> - <param name="generateSvg" argument="--generateSvg" type="boolean" checked="false" label="Generate SVG map" help="should the program generate an editable svg map of the processes?" /> - <param name="generatePdf" argument="--generatePdf" type="boolean" checked="true" label="Generate PDF map" help="should the program return a non editable (but displayble) pdf map of the processes?" /> - <param name="upRegCol" argument="--upRegCol" type="text" label="Up-regulated color" value="ecac68" help="Color for up-regulated reactions " /> - <param name="downRegCol" argument="--downRegCol" type="text" label="Down-regulated color" value="6495ed" help="Color for down-regulated reactions " /> - - <param name="netRPS" argument="--net" type="boolean" checked="false" label="Should RPS enrichment use net values?" help="If checked and RPS datasets are present the arrow tips of a reversible arrow will be colored with the net contribution of both directions' RPS values" /> - </when> - </conditional> - </inputs> - - <outputs> - <data format="txt" name="log" label="MaREA - Log" /> - <collection name="results" type="list" label="MaREA - Results"> - <discover_datasets pattern="__name_and_ext__" directory="result"/> - </collection> - </outputs> - - <help> - <![CDATA[ - -Overview -------------- - -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 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. -Row header: reaction ID. - -Optional files: - - 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 (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’). - -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 -------------- - -"RAS of group 1 + RAS of group 2 + ... + RAS of group N" option: - -RAS Dataset 1: - -+------------+----------------+----------------+----------------+ -| 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 | -+------------+----------------+----------------+----------------+ - -RAS 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 | -+------------+----------------+----------------+----------------+ - -"RAS of all samples + sample group specification" option: - -RAS Dataset: - -+------------+----------------+----------------+----------------+ -| 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 | -+------------+----------------+----------------+----------------+ - -Group-file - -+---------------+-----------+ -| Patient ID | Class | -+===============+===========+ -| TCGAAA3529 | MSI | -+---------------+-----------+ -| TCGAA62671 | MSS | -+---------------+-----------+ -| TCGAA62672 | MSI | -+---------------+-----------+ - -Advanced options ----------------- - -Statistical test: the statistical test to use for the analysis based on your data and the amount of replicates. The Kolmogorov-Smirnov test is the default option, but you can choose between T-test (paired), T-test (unpaired), Wilcoxon and Mann-Whitney tests. -P-Value threshold: the threshold used for significance in the selected 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 - -**TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_. - -.. class:: infomark - -**TIP**: If the user provide just one dataset for analysis: - -Use the Cluster Analysis tool to assign group labels when no prior division information is available - -provide an external group file specifying the assignment of each sample, if the group division is known a priori - -.. class:: infomark - -**TIP**: This tool using the RAS scores computed by Ras generator tool. - -@REFERENCE@ - -.. _Ras tool: http://bimib.disco.unimib.it:5555/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbimib%2Fmarea%2FMaREA+RAS+Generator%2F1.0.6&version=1.0.6&__identifer=auulv6gbp76 -.. _Convert delimiters to TAB: http://bimib.disco.unimib.it:5555/?tool_id=Convert+characters1&version=1.0.0&__identifer=76g7trea4j6 -.. _MaREA cluster analysis: http://bimib.disco.unimib.it:5555/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbimib%2Fmarea%2FMaREA_cluester%2F1.1.2&version=1.1.2&__identifer=lxbyzn2me9 - -]]> - </help> - <expand macro="citations" /> - -</tool>