Mercurial > repos > sybila > recetox_aplcms_unsupervised
changeset 0:3bdec3b22152 draft default tip
planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 7befebc7a9bc40d8b97f4dac752ad9646aac40de
| author | sybila |
|---|---|
| date | Fri, 09 Sep 2022 13:06:32 +0000 |
| parents | |
| children | |
| files | ebcsgen_generate_ts.py ebcsgen_generate_ts.xml macros.xml test-data/simple.bcsl.model |
| diffstat | 4 files changed, 125 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ebcsgen_generate_ts.py Fri Sep 09 13:06:32 2022 +0000 @@ -0,0 +1,43 @@ +import argparse + +from eBCSgen.Errors.ModelParsingError import ModelParsingError +from eBCSgen.Errors.UnspecifiedParsingError import UnspecifiedParsingError +from eBCSgen.Parsing.ParseBCSL import Parser + +import numpy as np + + +args_parser = argparse.ArgumentParser(description='Transition system generating') + +args_parser._action_groups.pop() +required = args_parser.add_argument_group('required arguments') +optional = args_parser.add_argument_group('optional arguments') + +required.add_argument('--model', type=str, required=True) +required.add_argument('--output', type=str, required=True) +required.add_argument('--direct', required=True) + +optional.add_argument('--max_time', type=float, default=np.inf) +optional.add_argument('--max_size', type=float, default=np.inf) +optional.add_argument('--bound', type=int, default=None) + +args = args_parser.parse_args() + +model_parser = Parser("model") +model_str = open(args.model, "r").read() + +model = model_parser.parse(model_str) +if model.success: + if eval(args.direct): + ts = model.data.generate_direct_transition_system(args.max_time, + args.max_size, + args.bound) + ts.change_to_vector_backend() + else: + vm = model.data.to_vector_model(args.bound) + ts = vm.generate_transition_system(None, args.max_time, args.max_size) + ts.save_to_json(args.output, model.data.params) +else: + if "error" in model.data: + raise UnspecifiedParsingError(model.data["error"]) + raise ModelParsingError(model.data, model_str)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ebcsgen_generate_ts.xml Fri Sep 09 13:06:32 2022 +0000 @@ -0,0 +1,58 @@ +<tool id="eBCSgen_generate_transition_system" name="eBCSgen - transition system generator" version="@TOOL_VERSION@_galaxy0"> + <description>- generate transition system of the 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 ${__tool_directory__}/ebcsgen_generate_ts.py + --model '$model' + --output '$output' + --direct '$network_free_choice' + #if $adv.bound != "": + --bound '$adv.bound' + #end if + #if $adv.max_time != "": + --max_time '$adv.max_time' + #end if + #if $adv.max_size != "": + --max_size '$adv.max_size' + #end if + </command> + + <inputs> + <param format="bcsl.model" name="model" type="data" label="Model file" help="Provide a BCSL model file"/> + <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> + <section name="adv" title="Advanced Options" expanded="false"> + <param name="bound" min="0" type="integer" value="" label="Bound [optional]" optional="true"/> + <param name="max_time" min="0" type="float" value="" + label="Maximal computation time (in seconds) [optional]" optional="true"/> + <param name="max_size" min="1" type="integer" value="" label="Maximal TS size [optional]" optional="true"/> + </section> + </inputs> + + <outputs> + <data label="Transition system of ${on_string}" format="bcsl.ts" name="output"/> + </outputs> + + <tests> + <test> + <param name="model" value="simple.bcsl.model" ftype="bcsl.model"/> + <output name="output" ftype="bcsl.ts"> + <assert_contents> + <has_text text="nodes"/> + <has_text text="edges"/> + <has_text text="ordering"/> + <has_text text="initial"/> + <has_n_lines n="98" /> + </assert_contents> + </output> + </test> + </tests> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Sep 09 13:06:32 2022 +0000 @@ -0,0 +1,17 @@ +<macros> + <token name="@TOOL_VERSION@">2.0.3</token> + + <xml name="creator"> + <creator> + <person + givenName="Matej" + familyName="Troják" + url="https://github.com/xtrojak" + identifier="0000-0003-0841-2707" /> + <organization + url="https://sybila.fi.muni.cz/" + email="sybila@fi.muni.cz" + name="SYBILA MUNI" /> + </creator> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/simple.bcsl.model Fri Sep 09 13:06:32 2022 +0000 @@ -0,0 +1,7 @@ +#! rules +r1_S ~ P(S{i})::cell => P(S{a})::cell +r1_T ~ P(T{i})::cell => P(T{a})::cell +r2 ~ P()::cell => P()::out + +#! inits +1 P(S{i},T{i})::cell \ No newline at end of file