Mercurial > repos > sybila > ebcsgen_pctl_parameter_synthesis

annotate ebcsgen_pctl_parameter_synthesis.xml @ 1:f280183d1289 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 83232805a8721c48078c88367e3480a5553f0182
author sybila
date Fri, 14 Oct 2022 16:25:57 +0000
parents cf609f659b21
children 3bb6c1e9252e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
1 <tool id="eBCSgen_PCTL_parameter_synthesis" name="eBCSgen PCTL parameter synthesis" version="@TOOL_VERSION@_galaxy0">
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
2 <description>- PCTL parameter synthesis of given parametric transition system</description>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
3 <macros>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
4 <import>macros.xml</import>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
5 </macros>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
6 <expand macro="creator"/>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
7 <requirements>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
8 <container type="docker">sybila/ebcsgen:v@TOOL_VERSION@</container>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
9 </requirements>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
10
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
11 <options sanitize="False"/>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
12 <command>python3 ${__tool_directory__}/ebcsgen_pctl_parameter_synthesis.py
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
13 --transition_file '$transition_file'
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
14 #if len($regions) > 0:
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
15 --output '$output_regions'
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
16 #else:
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
17 --output '$output_sample'
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
18 #end if
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
19 --formula '$formula'
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
20
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
21 #set parameters = ",".join([str($s.from) + "=" + str($s.param) + "=" + str($s.to) for $s in $regions])
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
22 #if $parameters:
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
23 --region '$parameters'
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
24 #end if
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
25 </command>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
26
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
27 <inputs>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
28 <param format="bcsl.ts" name="transition_file" type="data" label="Computed Transition system"/>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
29 <param name="formula" type="text" label="PCTL formula">
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
30 <validator type="empty_field"/>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
31 </param>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
32
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
33 <repeat name="regions" title="Parameter intervals">
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
34 <param name="param" value="" type="text" label="Parameter name:">
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
35 <validator type="empty_field"/>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
36 </param>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
37 <param name="from" type="float" value="" label="Interval start:"/>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
38 <param name="to" type="float" value="" label="Interval end:"/>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
39 </repeat>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
40 </inputs>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
41
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
42 <outputs>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
43 <data format="txt" name="output_regions">
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
44 <filter>"?" not in formula</filter>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
45 </data>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
46 <data format="storm.sample" name="output_sample">
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
47 <filter>"?" in formula</filter>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
48 </data>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
49 </outputs>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
50
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
51 <tests>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
52 <test>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
53 <param name="transition_file" value="parametrised.bcsl.ts" ftype="bcsl.ts"/>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
54 <param name="formula" value="P&lt;=0.2 [F P2(active{on})::cell &gt; 0]"/>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
55 <repeat name="regions">
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
56 <param name="param" value="param_sig"/>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
57 <param name="from" value="0.1"/>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
58 <param name="to" value="0.6"/>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
59 </repeat>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
60 <repeat name="regions">
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
61 <param name="param" value="param_block"/>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
62 <param name="from" value="0.05"/>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
63 <param name="to" value="1.0"/>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
64 </repeat>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
65 <output name="output_regions" ftype="txt">
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
66 <assert_contents>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
67 <has_text text="Region results:"/>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
68 </assert_contents>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
69 </output>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
70 </test>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
71 <test>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
72 <param name="transition_file" value="parametrised.bcsl.ts" ftype="bcsl.ts"/>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
73 <param name="formula" value="P=? [F P2(active{on})::cell &gt; 0]"/>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
74 <output name="output_sample" ftype="storm.sample">
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
75 <assert_contents>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
76 <has_text text="Result (initial states):"/>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
77 </assert_contents>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
78 </output>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
79 </test>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
80 </tests>
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
81
cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
sybila
parents:
diff changeset
82 </tool>