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comparison rpbasicdesign.xml @ 0:a9f519126d6a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign commit bdac148247c9c3d3da3420220d006e723c718277"
author iuc
date Wed, 30 Mar 2022 13:04:57 +0000
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1 <tool id="rpbasicdesign" name="BasicDesign" version="@TOOL_VERSION@" profile="21.09">
2 <description>Build DNA-BOT input files from rpSBML</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.0.1</token>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">rpbasicdesign</requirement>
8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[
10 python -m rpbasicdesign.cli
11 --rpsbml_file '$rpsbml_file'
12 #if $adv.parts_files
13 #set files = '" "'.join([str($file) for $file in $adv.parts_files])
14 --parts_files "${files}"
15 #end if
16 --lms_id '$adv.lms_id'
17 --lmp_id '$adv.lmp_id'
18 --backbone_id '$backbone_id'
19 --sample_size '$sample_size'
20 $adv.cds_permutation
21 --o_dnabot_dir 'out/dnabot_in'
22 $adv.sbol_output
23 --max_enz_per_rxn $adv.max_enz_per_rxn
24 ]]></command>
25 <inputs>
26 <param name="rpsbml_file" type="data" format="sbml" label="rpSBML file" help="SBML file from which enzymes UniProt IDs will be collected."/>
27 <param argument="--backbone_id" type="text" value="BASIC_SEVA_37_CmR-p15A.1" label="Backbone part ID" help="Part ID to be used as the backbone.">
28 <sanitizer invalid_char="">
29 <valid initial="string.letters,string.digits">
30 <add value=":" />
31 <add value="." />
32 <add value="-" />
33 <add value="_" />
34 </valid>
35 </sanitizer>
36 <validator type="empty_field" message="Backbone ID is required"/>
37 </param>
38 <param argument="--sample_size" type="integer" value="88" min="1" max="88" label="Sample size" help="Number of constructs to generate."/>
39 <section name="adv" title="Advanced Options" expanded="false">
40 <param name="parts_files" type="data" format="csv" optional="true" multiple="true" label="Linkers and user parts" help="List of files providing available linkers and user parts (backbone, promoters, ...) for constructs. Default: Standard Biolegio Parts (BBP-18500)" />
41 <param argument="--lms_id" type="text" value="LMS" label="LMS part ID" help="Part ID to be used as the LMS methylated linker." >
42 <sanitizer invalid_char="">
43 <valid initial="string.letters,string.digits">
44 <add value=":" />
45 <add value="-" />
46 <add value="_" />
47 <add value="." />
48 </valid>
49 </sanitizer>
50 <validator type="empty_field" message="LMS ID is required"/>
51 </param>
52 <param argument="--lmp_id" type="text" value="LMP" label="LMP part ID" help="Part ID to be used as the LMP methylated linker.">
53 <sanitizer invalid_char="">
54 <valid initial="string.letters,string.digits">
55 <add value=":" />
56 <add value="-" />
57 <add value="_" />
58 <add value="." />
59 </valid>
60 </sanitizer>
61 <validator type="empty_field" message="LMP ID is required"/>
62 </param>
63 <param argument="--cds_permutation" type="boolean" truevalue="--cds_permutation true" falsevalue="--cds_permutation false" checked="true" label="Perform CDS permutation?" help="Whether all combinations of CDS permutation should be built." />
64 <param argument="--sbol_output" type="boolean" checked="false" truevalue="--o_sbol_dir out/sbol_export" falsevalue="" label="Output SBOL results?" help="Whether SBOL (Synthetic Biology Open Language) depictions of constructs should be outputted" />
65 <param argument="--max_enz_per_rxn" type="integer" value="1" min="1" max="99" label="Maximum number of enyzme to consider per reaction." help="Maximum number of enyzme to consider per reaction. If more enzymes are available for a given reaction, then only the last one listed in the MIRIAM annotation section will be kept."/>
66 </section>
67 </inputs>
68 <outputs>
69 <data name="Constructs" format="csv" from_work_dir="out/dnabot_in/constructs.csv" label="${tool.name} on ${rpsbml_file.name}: constructs" />
70 <data name="User_parts_plate" format="csv" from_work_dir="out/dnabot_in/user_parts_plate.csv" label="${tool.name} on ${rpsbml_file.name}: User parts plate"/>
71 <data name="Biolegio_plate" format="csv" from_work_dir="out/dnabot_in/biolegio_plate.csv" label="${tool.name} on ${rpsbml_file.name}: Biolegio plate"/>
72 <collection name="sbol_dir" type="list" label="${tool.name} on ${rpsbml_file.name}: SBOL constructs">
73 <filter> adv['sbol_output'] </filter>
74 <discover_datasets pattern="__designation_and_ext__" format="xml" directory="out/sbol_export" />
75 </collection>
76 </outputs>
77 <tests>
78 <test expect_num_outputs="4">
79 <!-- test 1: check if identical outputs are produced (Lycopene input)-->
80 <param name="rpsbml_file" value="lycopene_CrtEBI_from_selenzy.xml" />
81 <param name="sample_size" value="3" />
82 <output name="Constructs" file="constructs_lycopene.csv" ftype="csv" compare="diff">
83 <assert_contents>
84 <has_n_lines n="4"/>
85 </assert_contents>
86 </output>
87 <output name="User_parts_plate" file="user_parts_plate_lycopene.csv" ftype="csv" compare="diff"/>
88 <output name="Biolegio_plate" file="biolegio_plate_lycopene.csv" ftype="csv" compare="diff"/>
89 <param name="sbol_output" value="true" />
90 <output_collection name="sbol_dir" type="list" count="3">
91 <element name="BASIC_construct_A1">
92 <assert_contents>
93 <is_valid_xml />
94 <has_text text="BASIC_construct_A1" />
95 <has_n_lines n="339" />
96 </assert_contents>
97 </element>
98 <element name="BASIC_construct_B1">
99 <assert_contents>
100 <is_valid_xml />
101 <has_text text="BASIC_construct_B1" />
102 <has_n_lines n="339" />
103 </assert_contents>
104 </element>
105 <element name="BASIC_construct_C1">
106 <assert_contents>
107 <is_valid_xml />
108 <has_text text="BASIC_construct_C1" />
109 <has_n_lines n="339" />
110 </assert_contents>
111 </element>
112 </output_collection>
113 </test>
114 <test expect_num_outputs="3">
115 <!-- test 2: check if identical outputs are produced (Muconate input)-->
116 <param name="rpsbml_file" value="muconate_example.xml" />
117 <param name="sample_size" value="88" />
118 <output name="Constructs" file="constructs_muconate.csv" ftype="csv" compare="diff">
119 <assert_contents>
120 <has_n_lines n="89"/>
121 </assert_contents>
122 </output>
123 <output name="User_parts_plate" file="user_parts_plate_muconate.csv" ftype="csv" compare="diff"/>
124 <output name="Biolegio_plate" file="biolegio_plate_muconate.csv" ftype="csv" compare="diff"/>
125 </test>
126 </tests>
127 <help><![CDATA[
128 rpbasicdesign
129 ================
130
131 rpbasicdesign extracts enzyme IDs from rpSBML (System Biology Markup Language) files containing additionnal annotations (e.g. reaction rules ID) and produced by the RP (RetroPath) suite available in `SynBioCAD Galaxy platform <https://galaxy-synbiocad.org/>`_, to generate genetic constructs compliant with the BASIC (Biopart Assembly Standard for Idempotent Cloning) assembly approach. CSV files produced are ready to be used with DNA-Bot to generate instructions for automated build of the genetic constructs using OpenTrons liquid handling robots.
132
133 Input
134 -----
135
136 Required:
137
138 * **rpSBML file**\ : rpSBML file from which enzymes UniProt IDs will be collected.
139
140 Advanced options:
141
142 * **Linkers and user parts**\ : (string) List of files providing available linkers and user parts (backbone, promoters, ...) for constructs. Default: ( `Standard Biolegio Parts <https://www.biolegio.com/>`_: BBP-18500).
143 * **LMS part ID**\ : (string) part ID to be used as the LMS methylated linker. Default: LMS.
144 * **LMP part ID**\ : (string) part ID to be used as the LMP methylated linker. Default: LMP.
145 * **Backbone part ID**\ : (string) part ID to be used as the backbone. Default: BASIC_SEVA_37_CmR-p15A.1.
146 * **Sample size**\ : (int) Number of constructs to generate. Default: 88.
147 * **Perform CDS permutation?**\ : (boolean) Whether all combinations of CDS permutation should be built Default: true.
148 * **Maximum number of enyzme to consider per reaction**\ : (int) Maximum number of enyzme to consider per reaction. If more enzymes are available for a given reaction, then only the last one listed in the MIRIAM annotation section will be kept. (Default: 1).
149
150 Output
151 ------
152
153 * **constructs**\ : CSV construct file listing the constructs to be built.
154 * **User parts plate**\ : CSV file listing the DNA parts to be included into each construct.
155 * **Biolegio plate**\ : CSV file listing the plate coordinates of the BASIC linkers.
156 * **SBOL constructs**\ : (optional) one SBOL (Synthetic Biology Open Language) file is produced for each construct generated in XML format.
157
158 Project Links
159 ------------------
160
161 * `GitHub <https://github.com/brsynth/rpbasicdesign>`_
162
163 License
164 -------
165
166 * `MIT <https://github.com/brsynth/rpbasicdesign/blob/master/LICENSE.txt>`_
167
168 ]]></help>
169 <citations>
170 <citation type="doi">10.1093/synbio/ysaa010</citation>
171 </citations>
172 </tool>