Mercurial > repos > sybila > ebcsgen_simulation
diff ebcsgen_simulate.xml @ 0:179d32e79968 draft
planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 33b83dc8c71401922b087400fa1f4080e9abe170
author | sybila |
---|---|
date | Tue, 04 Oct 2022 13:15:48 +0000 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ebcsgen_simulate.xml Tue Oct 04 13:15:48 2022 +0000 @@ -0,0 +1,96 @@ +<tool id="eBCSgen_simulate" name="eBCSgen simulation" version="@TOOL_VERSION@_galaxy0"> + <description>- simulate given model</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="creator"/> + <requirements> + <container type="docker">sybila/ebcsgen:v@TOOL_VERSION@</container> + </requirements> + + <command>python3 ${__tool_directory__}/ebcsgen_simulate.py + --model '$model' + --output '$output' + --deterministic '$type.deterministic_choice' + #if $type.deterministic_choice == "True": + --direct False + --runs 1 + --volume '$type.volume' + --step '$type.step' + #else: + --direct '$type.network_free_choice' + --runs '$type.num_of_runs' + --volume 1 + --step 0.01 + #end if + --max_time '$max_time' + </command> + + <inputs> + <param format="bcsl.model" name="model" type="data" label="Model file" help="Provide a BCSL model file"/> + <conditional name="type"> + <param name="deterministic_choice" type="select" label="Choose simulation method:"> + <option value="False" selected="true">Stochastic</option> + <option value="True">Deterministic</option> + </param> + <when value="False"> + <param name="network_free_choice" type="select" label="Choose network-free approach:"> + <option value="False" selected="true">Indirect</option> + <option value="True">Direct</option> + </param> + <param name="num_of_runs" min="1" type="integer" value="1" label="Number of runs:"/> + </when> + <when value="True"> + <param name="volume" min="0" type="integer" value="1" label="Volume (liters):"/> + <param name="step" min="0" type="float" value="0.01" label="Simulation step:"/> + </when> + </conditional> + <param name="max_time" min="0" type="integer" value="1" label="Maximum simulation time:"/> + </inputs> + + <outputs> + <data format="csv" name="output"/> + </outputs> + + <tests> + <test> + <param name="model" value="repressilator.bcsl.model" ftype="bcsl.model"/> + <section name="type"> + <param name="deterministic_choice" value="True"/> + <param name="step" value="0.1"/> + </section> + <param name="max_time" value="100"/> + <output name="output" value="simulation_determ.csv" ftype="csv"/> + </test> + <test> + <param name="model" value="repressilator.bcsl.model" ftype="bcsl.model"/> + <section name="type"> + <param name="deterministic_choice" value="False"/> + <param name="network_free_choice" value="False"/> + <param name="num_of_runs" value="2"/> + </section> + <param name="max_time" value="200"/> + <output name="output" ftype="csv"> + <assert_contents> + <has_n_columns n="4" sep=","/> + <has_n_lines min="10"/> + </assert_contents> + </output> + </test> + <test> + <param name="model" value="repressilator.bcsl.model" ftype="bcsl.model"/> + <section name="type"> + <param name="deterministic_choice" value="False"/> + <param name="network_free_choice" value="True"/> + <param name="num_of_runs" value="1"/> + </section> + <param name="max_time" value="100"/> + <output name="output" ftype="csv"> + <assert_contents> + <has_n_columns n="4" sep=","/> + <has_n_lines min="10"/> + </assert_contents> + </output> + </test> + </tests> +</tool>