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view erecord_file.xml @ 6:8ac7eb55f387 draft
planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 8b48fe16048d42404b01076a970258d093fe6d17-dirty
author | siwaa |
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date | Thu, 15 Feb 2024 17:24:53 +0000 |
parents | 9e8f5f220917 |
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<tool id="erecord_file" name="erecord_file" version="1.0.0"> <description>erecord returning .json + maybe .zip or .xls</description> <requirements> <!-- singularity --> <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/erecord-deploy/rep_recordb:9d6ea1defd50dd63fe036a7545a9ea527572192e</container> <!-- image locale --> <!-- container type="singularity">/home/nrousse/workspace_git/SIWAA_regroup/erecord-deploy/containers/_fab_SIMG/rep_recordb.simg</container--> </requirements> <command detect_errors="aggressive"> <![CDATA[ . /PYVENV/bin/activate; echo "action_name VAUT $request_condition.action_name"; #if $request_condition.action_name == 'post_vpz_experiment': /bin/bash -c "python3 $__tool_directory__/main_file.py -action ${request_condition.action_name} -data ${input_json} -datafolder ${datafolder} -experimentfile ${experimentfile}"; #elif $request_condition.action_name == 'post_vpz_report': /bin/bash -c "python3 $__tool_directory__/main_file.py -action ${request_condition.action_name} -data ${input_json} -datafolder ${datafolder}"; #elif $request_condition.action_name == 'post_vpz_output': /bin/bash -c "python3 $__tool_directory__/main_file.py -action ${request_condition.action_name} -data ${input_json} -datafolder ${datafolder}"; #elif $request_condition.action_name == 'post_vpz_inout': /bin/bash -c "python3 $__tool_directory__/main_file.py -action ${request_condition.action_name} -data ${input_json} -datafolder ${datafolder}"; #else: /bin/bash -c "python3 $__tool_directory__/main_file.py -action ${request_condition.action_name} -data ${input_json}"; #end if cp WS/OUT/output.json ${output_json}; #if $request_condition.action_name == 'get_vpz_experiment': touch WS/OUT/experiment.xls; cp WS/OUT/experiment.xls ${experiment}; #elif $request_condition.action_name == 'post_vpz_experiment': touch WS/OUT/experiment.xls; cp WS/OUT/experiment.xls ${experiment}; #elif $request_condition.action_name == 'get_vpz_report_conditions': touch WS/OUT/conditions.xls; cp WS/OUT/conditions.xls ${conditions}; #elif $request_condition.action_name == 'post_vpz_report_conditions': touch WS/OUT/conditions.xls; cp WS/OUT/conditions.xls ${conditions}; #elif $request_condition.action_name == 'get_vpz_report': touch WS/OUT/report.zip; cp WS/OUT/report.zip ${report}; #elif $request_condition.action_name == 'post_vpz_report': touch WS/OUT/report.zip; cp WS/OUT/report.zip ${report}; #end if ]]> </command> <inputs> <param name="input_json" optional="true" type="data" format="json" label="Input json file"/> <conditional name="request_condition"> <param name="action_name" type="select" label="Select action"> <option value="help" selected="true">help</option> <option value="get_pkg_list">get_pkg_list</option> <option value="get_pkg_vpz_list">get_pkg_vpz_list</option> <option value="get_pkg_data_list">get_pkg_data_list</option> <option value="get_vpz_input">get_vpz_input</option> <option value="post_vpz_input">post_vpz_input</option> <option value="get_vpz_output">get_vpz_output</option> <option value="post_vpz_output">post_vpz_output</option> <option value="get_vpz_inout">get_vpz_inout</option> <option value="post_vpz_inout">post_vpz_inout</option> <option value="get_vpz_experiment">get_vpz_experiment</option> <option value="post_vpz_experiment">post_vpz_experiment</option> <option value="get_vpz_report">get_vpz_report</option> <option value="post_vpz_report">post_vpz_report</option> <option value="get_vpz_report_conditions">get_vpz_report_conditions</option> <option value="post_vpz_report_conditions">post_vpz_report_conditions</option> </param> <when value="post_vpz_experiment"> <param name="experimentfile" type="data" format="csv,xls" label="Add a experiment xls (csv) file" help="experimentfile from gest_vpz_experiment + modifications"/> <param name="datafolder" optional="true" type="data" format="zip" label="Add a datafolder zip file" help="Precisions sur forme du dossier..."/> </when> <when value="post_vpz_report"> <param name="datafolder" optional="true" type="data" format="zip" label="Add a datafolder zip file" help="Precisions sur forme du dossier..."/> </when> <when value="post_vpz_output"> <param name="datafolder" optional="true" type="data" format="zip" label="Add a datafolder zip file" help="Precisions sur forme du dossier..."/> </when> <when value="post_vpz_inout"> <param name="datafolder" optional="true" type="data" format="zip" label="Add a datafolder zip file" help="Precisions sur forme du dossier..."/> </when> <when value="get_vpz_experiment" /> <when value="get_vpz_report_conditions" /> <when value="post_vpz_report_conditions"/> <when value="get_vpz_report" /> <when value="get_vpz_input" /> <when value="post_vpz_input" /> <when value="get_vpz_output" /> <when value="get_vpz_inout" /> <when value="get_pkg_list" /> <when value="get_pkg_vpz_list" /> <when value="get_pkg_data_list" /> <when value="help" /> </conditional> </inputs> <outputs> <data name="output_json" format="json" label="output_json"/> <data name="experiment" format="xls" label="experiment"> <filter>request_condition['action_name'] == 'get_vpz_experiment' or request_condition['action_name'] == 'post_vpz_experiment'</filter> </data> <data name="conditions" format="xls" label="conditions.xls file"> <filter>request_condition['action_name'] == 'get_vpz_report_conditions' or request_condition['action_name'] == 'post_vpz_report_conditions'</filter> </data> <data name="report" format="zip" label="report"> <filter>request_condition['action_name'] == 'get_vpz_report' or request_condition['action_name'] == 'post_vpz_report'</filter> </data> </outputs> <tests> </tests> <help><![CDATA[ erecord_file.xml ================ Actions: ------- - 'help' - 'get_pkg_list' 'get_pkg_vpz_list' 'get_pkg_data_list' - 'get_vpz_input' 'post_vpz_input' - 'get_vpz_output' 'post_vpz_output' - 'get_vpz_inout' 'post_vpz_inout' - 'get_vpz_experiment' 'post_vpz_experiment' - 'get_vpz_report_conditions' 'post_vpz_report_conditions' - 'get_vpz_report' 'post_vpz_report' Code: ---- - main_file.py Inputs: ------- - action value (mandatory) - data json file (optional) (json file, param type="data") An action value that would be into data would be ignored - experiment.xls (only in 'post_vpz_experiment' case) - datafolder (optional) (only in cases : 'post_vpz_experiment', 'post_vpz_report', 'post_vpz_output', 'post_vpz_inout') Outputs: -------- - data json file - 1 other file (xls or zip) : - if 'action' == get_vpz_experiment, post_vpz_experiment : experiment.xls file - if 'action' == get_vpz_report_conditions, post_vpz_report_conditions : conditions.xls file - if 'action' == get_vpz_report, post_vpz_report : report.zip file Credits: -------- - Author: Nathalie Rousse nathalie.rousse@inrae.fr - Copyright: INRAE ]]> </help> </tool>