# HG changeset patch
# User sybila
# Date 1664889348 0
# Node ID 179d32e79968addadc776593bffb42a274e47156

planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 33b83dc8c71401922b087400fa1f4080e9abe170

diff -r 000000000000 -r 179d32e79968 ebcsgen_simulate.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ebcsgen_simulate.py	Tue Oct 04 13:15:48 2022 +0000
@@ -0,0 +1,51 @@
+import argparse
+
+from eBCSgen.Errors import UnspecifiedParsingError
+from eBCSgen.Errors.InvalidInputError import InvalidInputError
+from eBCSgen.Errors.ModelParsingError import ModelParsingError
+from eBCSgen.Errors.RatesNotSpecifiedError import RatesNotSpecifiedError
+from eBCSgen.Parsing.ParseBCSL import Parser
+
+
+args_parser = argparse.ArgumentParser(description='Simulation')
+
+args_parser._action_groups.pop()
+required = args_parser.add_argument_group('required arguments')
+
+required.add_argument('--model', type=str, required=True)
+required.add_argument('--output', type=str, required=True)
+required.add_argument('--deterministic', required=True)
+required.add_argument('--direct', required=True)
+required.add_argument('--runs', type=int, required=True)
+required.add_argument('--max_time', type=float, required=True)
+required.add_argument('--volume', type=float, required=True)
+required.add_argument('--step', type=float, required=True)
+
+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 len(model.data.params) != 0:
+        raise InvalidInputError("Provided model is parametrised - simulation cannot be executed.")
+    if not model.data.all_rates:
+        raise RatesNotSpecifiedError("Some rules do not have rates specified - simulation cannot be executed.")
+
+    if eval(args.deterministic):
+        vm = model.data.to_vector_model()
+        df = vm.deterministic_simulation(args.max_time, args.volume, args.step)
+    else:
+        if eval(args.direct):
+            df = model.data.network_free_simulation(args.max_time)
+        else:
+            vm = model.data.to_vector_model()
+            df = vm.stochastic_simulation(args.max_time, args.runs)
+
+    df.to_csv(args.output, index=None, header=True)
+else:
+    if "error" in model.data:
+        raise UnspecifiedParsingError(model.data["error"])
+    raise ModelParsingError(model.data, model_str)
diff -r 000000000000 -r 179d32e79968 ebcsgen_simulate.xml
--- /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>
diff -r 000000000000 -r 179d32e79968 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Oct 04 13:15:48 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>
diff -r 000000000000 -r 179d32e79968 test-data/repressilator.bcsl.model
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/repressilator.bcsl.model	Tue Oct 04 13:15:48 2022 +0000
@@ -0,0 +1,15 @@
+#! rules
+X()::rep => @ k1*[X()::rep]
+Y()::rep => @ k2*[Y()::rep]
+Z()::rep => @ k1*[Z()::rep]
+ => X()::rep @ 5**4/(5**4+[Z()::rep]**4)
+ => Y()::rep @ 5**4/(5**4+[X()::rep]**4)
+ => Z()::rep @ 5**4/(5**4+[Y()::rep]**4)
+
+#! inits
+1 X()::rep
+1 Y()::rep
+
+#! definitions
+k1 = 0.05
+k2 = 0.12
diff -r 000000000000 -r 179d32e79968 test-data/simulation_determ.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/simulation_determ.csv	Tue Oct 04 13:15:48 2022 +0000
@@ -0,0 +1,1002 @@
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