Mercurial > repos > tduigou > rpreport
changeset 0:d09a51507aaf draft
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
| author | tduigou |
|---|---|
| date | Mon, 14 Feb 2022 14:23:00 +0000 |
| parents | |
| children | 3ea8aa1e94b4 |
| files | rpreport.xml test-data/input_rpSBML.tar test-data/rpreport_output.html |
| diffstat | 3 files changed, 224 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rpreport.xml Mon Feb 14 14:23:00 2022 +0000 @@ -0,0 +1,97 @@ +<tool id="rpreport" name="Pathways HTML Report" version="@TOOL_VERSION@" profile="19.09"> + <description>Generates HTML report to explore the main characteristics of pathways +predicted with RetroPath suite</description> + <macros> + <token name="@TOOL_VERSION@">5.12.1</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">rptools</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + #if str($input_type_conditional.input_type) == "sbml": + cd /tmp && + #set input_folder="tmp_folder" + mkdir -p '$input_folder' && + #for $input in $input_type_conditional.input_sbml.keys(): + ln -sfn $input_type_conditional.input_sbml[$input] '$input_folder/$input'; + #end for + python -m rptools.rpreport -d '$input_folder' + #elif str($input_type_conditional.input_type) == "tar": + python -m rptools.rpreport '${input_type_conditional.input_tar}' + #end if + '$html_file.files_path' + && cp '$html_file.files_path'/index.html '$html_file' + ]]></command> + <inputs> + <conditional name="input_type_conditional"> + <param name="input_type" type="select" label="Source SBML format"> + <option value="tar" selected="True">TAR</option> + <option value="sbml">Collection</option> + </param> + <when value="tar"> + <param name="input_tar" type="data" format="tar" label="Source SBML" /> + </when> + <when value="sbml"> + <param name="input_sbml" type="data_collection" format="xml" collection_type="list" label="Source SBML" /> + </when> + </conditional> + </inputs> + <outputs> + <data name="html_file" format="html" label="Pathways HTML Report"/> + </outputs> + <tests> + <test> + <!-- test 2: check if identical html output is produced (tar input) --> + <conditional name="input_type_conditional"> + <param name="input_type" value="tar"/> + <param name="input_tar" value="input_rpSBML.tar" /> + </conditional> + <output name="html_file" file="rpreport_output.html" compare="diff"/> + </test> + </tests> + <help><![CDATA[ +rpReport +========= + +Generates HTML pages to explore the main characteristics (thermodynamics, +fluxes, number of metabolic steps, reaction rule score) of pathways predicted +with RetroPath suite + + +Input +----- + +Required: + +* **source_path**: (string) Path to a tar archive (default) or folder (using '-d' option) containing rpSBML file(s). + +Output +------ +* **output_folder**: (string) Output folder where report file(s) will be generated. + +Project Links +--------------------- +* `GitHub <https://github.com/brsynth/rptools>`_ + +Version +---------- + +5.12.1 + +Authors +------- + +* **Olivier Telle** + +Acknowledgments +--------------- + +* Thomas Duigou +* Joan Hérisson + +Licence +------- + +`MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_ + ]]></help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rpreport_output.html Mon Feb 14 14:23:00 2022 +0000 @@ -0,0 +1,127 @@ +<!DOCTYPE html> +<html lang="en"> +<head> + <!-- Required meta tags --> + <meta charset="UTF-8"> + <meta name="viewport" content="width=device-width, initial-scale=1"> + + <!-- Bootstrap CSS --> + <link rel="stylesheet" href="./css/bootstrap.min.css"> + + <!-- AG Grid scripts and CSS--> + <script src="./js/ag-grid-community.min.noStyle.js"></script> + <link rel="stylesheet" href="./css/ag-grid.min.css"> + <link rel="stylesheet" href="./css/ag-theme-alpine.min.css"> + <!-- AG Chart scripts --> + <script src="./js/ag-charts-community.min.js"></script> + <script src="./js/data.js"></script> + + <title>rpReport</title> +</head> + +<body> + <div class="container"> + <div class="row d-print-none"> + <div class="col"> + <div id="myGrid" style="width: 100%; height: 400px;" class="ag-theme-alpine"></div> + </div> + </div> + <!-- Selected row(s) only schown on print display --> + <div class="row d-none d-print-block"> + <div class="col"> + <div id="selectedRowOnPrint" class="table-responsive"></div> + </div> + </div> + + <div class="row"> + <div class="col"> + <p class="h4 bg-light text-center">Pathway details</p> + </div> + </div> + <div class="row gy-2"> + <div class="col-md-6"> + <div class="accordion" id="thermodynamic_chart_panel"> + <div class="accordion-item"> + <h2 class="accordion-header" id="headingTwo"> + <button class="accordion-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseTwo"> + Thermodynamic profile chart + </button> + </h2> + <div id="collapseTwo" class="accordion-collapse collapse"> + <div class="accordion-body"> + <!-- Thermodynamique profile chart here --> + <div id="dfG_prime_chart" style="height:300px"></div> + </div> + </div> + </div> + </div> + </div> + <div class="col-md-6"> + <div class="accordion" id="rule_score_chart_panel"> + <div class="accordion-item"> + <h2 class="accordion-header" id="headingThree"> + <button class="accordion-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseThree"> + Rule score chart + </button> + </h2> + <div id="collapseThree" class="accordion-collapse collapse"> + <div class="accordion-body"> + <!-- Pathway rule score chart here --> + <div id="rule_score_chart" style="height:300px"></div> + </div> + </div> + </div> + </div> + </div> + <div class="col-md-6"> + <div class="accordion" id="ec_code_panel"> + <div class="accordion-item"> + <h2 class="accordion-header" id="headingOne"> + <button class="accordion-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseOne"> + EC number(s) + </button> + </h2> + <div id="collapseOne" class="accordion-collapse collapse"> + <div class="accordion-body"> + <!-- Retropathway ec_codes list here --> + <div id="ec_code_details"></div> + </div> + </div> + </div> + </div> + </div> + </div> + <div class="row d-none" id="comparative_chart_panel"> + <div class="col"> + <div class="accordion"> + <div class="accordion-item"> + <h2 class="accordion-header" id="headingFour"> + <button class="accordion-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseFour"> + Comparative charts + </button> + </h2> + <div id="collapseFour" class="accordion-collapse collapse show"> + <div class="accordion-body"> + <!-- Comparative charts here --> + <div class="row"> + <div class="col-md-6" id="global_score_compar_chart" style="height:300px"></div> + <div class="col-md-6" id="fba_compar_chart" style="height:300px"></div> + <div class="col-md-6" id="dfg_compar_chart" style="height:300px"></div> + <div class="col-md-6" id="rule_score_compar_chart" style="height:300px"></div> + <div class="col-md-6" id="reactions_nb_compar_chart" style="height:300px"></div> + </div> + </div> + </div> + </div> + </div> + </div> + </div> + </div> + + <script src="./js/main.js"></script> + + <!-- Bootstrap Bundle (includes Popper) --> + <script src="./js/bootstrap.bundle.min.js"></script> + +</body> +</html>