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comparison rpbasicdesign.xml @ 3:e4821c820f7c draft

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"planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
author tduigou
date Wed, 30 Mar 2022 09:04:23 +0000
parents 8a087d7546b8
children 9ba4dab7f0ba
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2:8a087d7546b8 3:e4821c820f7c
1 <tool id="rpbasicdesign" name="BasicDesign" version="@TOOL_VERSION@" profile="19.09"> 1 <tool id="rpbasicdesign" name="BasicDesign" version="@TOOL_VERSION@" profile="21.09">
2 <description>Build DNA-BOT input files from rpSBML</description> 2 <description>Build DNA-BOT input files from rpSBML</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.0.1</token> 4 <token name="@TOOL_VERSION@">1.0.1</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
21 --o_dnabot_dir 'out/dnabot_in' 21 --o_dnabot_dir 'out/dnabot_in'
22 $adv.sbol_output 22 $adv.sbol_output
23 --max_enz_per_rxn $adv.max_enz_per_rxn 23 --max_enz_per_rxn $adv.max_enz_per_rxn
24 ]]></command> 24 ]]></command>
25 <inputs> 25 <inputs>
26 <param name="rpsbml_file" type="data" format="xml" label="rpSBML file" help="SBML file from which enzymes UniProt IDs will be collected."/> 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."> 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=""> 28 <sanitizer invalid_char="">
29 <valid initial="string.letters,string.digits"> 29 <valid initial="string.letters,string.digits">
30 <add value=":" /> 30 <add value=":" />
31 <add value="." /> 31 <add value="." />
32 <add value="-" /> 32 <add value="-" />
33 <add value="_" /> 33 <add value="_" />
34 </valid> 34 </valid>
35 </sanitizer> 35 </sanitizer>
36 <validator type="empty_field" message="Backbone ID is required"/> 36 <validator type="empty_field" message="Backbone ID is required"/>
37 <validator type="regex">[0-9a-zA-Z_:-]+</validator>
38 </param> 37 </param>
39 <param argument="--sample_size" type="integer" value="88" min="1" max="88" label="Number of constructs to generate" help="Number of construct to generate."/> 38 <param argument="--sample_size" type="integer" value="88" min="1" max="88" label="Sample size" help="Number of construct to generate."/>
40 <section name="adv" title="Advanced Options" expanded="false"> 39 <section name="adv" title="Advanced Options" expanded="false">
41 <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" /> 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)" />
42 <param argument="--lms_id" type="text" value="LMS" label="LMS part ID" help="Part ID to be used as the LMS methylated linker." > 41 <param argument="--lms_id" type="text" value="LMS" label="LMS part ID" help="Part ID to be used as the LMS methylated linker." >
43 <sanitizer invalid_char=""> 42 <sanitizer invalid_char="">
44 <valid initial="string.letters,string.digits"> 43 <valid initial="string.letters,string.digits">
45 <add value=":" /> 44 <add value=":" />
46 <add value="-" /> 45 <add value="-" />
60 </valid> 59 </valid>
61 </sanitizer> 60 </sanitizer>
62 <validator type="empty_field" message="LMP ID is required"/> 61 <validator type="empty_field" message="LMP ID is required"/>
63 </param> 62 </param>
64 <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." /> 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." />
65 <param argument="--sbol_output" type="boolean" checked="false" truevalue="--o_sbol_dir out/sbol_export" falsevalue="" label="Output SBOL results?" help="Output folder to write SBOL depictions of constructs." /> 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" />
66 <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."/> 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."/>
67 </section> 66 </section>
68 </inputs> 67 </inputs>
69 <outputs> 68 <outputs>
70 <data name="Constructs" format="csv" from_work_dir="out/dnabot_in/constructs.csv" label="${tool.name} on ${rpsbml_file.name}: constructs" /> 69 <data name="Constructs" format="csv" from_work_dir="out/dnabot_in/constructs.csv" label="${tool.name} on ${rpsbml_file.name}: constructs" />
71 <data name="User parts plate" format="csv" from_work_dir="out/dnabot_in/user_parts_plate.csv" label="${tool.name} on ${rpsbml_file.name}: User parts plate"/> 70 <data name="User_parts_plate" format="csv" from_work_dir="out/dnabot_in/user_parts_plate.csv" label="${tool.name} on ${rpsbml_file.name}: User parts plate"/>
72 <data name="Biolegio plate" format="csv" from_work_dir="out/dnabot_in/biolegio_plate.csv" label="${tool.name} on ${rpsbml_file.name}: Biolegio plate"/> 71 <data name="Biolegio_plate" format="csv" from_work_dir="out/dnabot_in/biolegio_plate.csv" label="${tool.name} on ${rpsbml_file.name}: Biolegio plate"/>
73 <collection name="sbol_dir" type="list" label="${tool.name} on ${rpsbml_file.name}: SBOL constructs"> 72 <collection name="sbol_dir" type="list" label="${tool.name} on ${rpsbml_file.name}: SBOL constructs">
74 <filter> adv['sbol_output'] </filter> 73 <filter> adv['sbol_output'] </filter>
75 <discover_datasets pattern="__designation_and_ext__" format="xml" directory="out/sbol_export" /> 74 <discover_datasets pattern="__designation_and_ext__" format="xml" directory="out/sbol_export" />
76 </collection> 75 </collection>
77 </outputs> 76 </outputs>
78 <tests> 77 <tests>
79 <test> 78 <test expect_num_outputs="4">
80 <!-- test 1: check if identical outputs are produced (Lycopene input)--> 79 <!-- test 1: check if identical outputs are produced (Lycopene input)-->
81 <param name="rpsbml_file" value="lycopene_CrtEBI_from_selenzy.xml" /> 80 <param name="rpsbml_file" value="lycopene_CrtEBI_from_selenzy.xml" />
82 <param name="sample_size" value="3" /> 81 <param name="sample_size" value="3" />
83 <output name="Constructs" file="constructs_lycopene.csv" ftype="csv" compare="diff"> 82 <output name="Constructs" file="constructs_lycopene.csv" ftype="csv" compare="diff">
84 <assert_contents> 83 <assert_contents>
85 <has_n_lines n="4"/> 84 <has_n_lines n="4"/>
86 </assert_contents> 85 </assert_contents>
87 </output> 86 </output>
88 <output name="User parts plate" file="user_parts_plate_lycopene.csv" ftype="csv" compare="diff"/> 87 <output name="User_parts_plate" file="user_parts_plate_lycopene.csv" ftype="csv" compare="diff"/>
89 <output name="Biolegio plate" file="biolegio_plate_lycopene.csv" ftype="csv" compare="diff"/> 88 <output name="Biolegio_plate" file="biolegio_plate_lycopene.csv" ftype="csv" compare="diff"/>
90 <param name="sbol_output" value="--o_sbol_dir out/sbol_export" /> 89 <param name="sbol_output" value="true" />
91 <output_collection name="sbol_dir" type="list" count="3"> 90 <output_collection name="sbol_dir" type="list" count="3">
92 <element name="BASIC_construct_A1"> 91 <element name="BASIC_construct_A1">
93 <assert_contents> 92 <assert_contents>
94 <is_valid_xml /> 93 <is_valid_xml />
95 <has_text text="BASIC_construct_A1" /> 94 <has_text text="BASIC_construct_A1" />
110 <has_n_lines n="339" /> 109 <has_n_lines n="339" />
111 </assert_contents> 110 </assert_contents>
112 </element> 111 </element>
113 </output_collection> 112 </output_collection>
114 </test> 113 </test>
115 <test> 114 <test expect_num_outputs="3">
116 <!-- test 2: check if identical outputs are produced (Muconate input)--> 115 <!-- test 2: check if identical outputs are produced (Muconate input)-->
117 <param name="rpsbml_file" value="muconate_example.xml" /> 116 <param name="rpsbml_file" value="muconate_example.xml" />
118 <param name="sample_size" value="88" /> 117 <param name="sample_size" value="88" />
119 <output name="Constructs" file="constructs_muconate.csv" ftype="csv" compare="diff"> 118 <output name="Constructs" file="constructs_muconate.csv" ftype="csv" compare="diff">
120 <assert_contents> 119 <assert_contents>
121 <has_n_lines n="89"/> 120 <has_n_lines n="89"/>
122 </assert_contents> 121 </assert_contents>
123 </output> 122 </output>
124 <output name="User parts plate" file="user_parts_plate_muconate.csv" ftype="csv" compare="diff"/> 123 <output name="User_parts_plate" file="user_parts_plate_muconate.csv" ftype="csv" compare="diff"/>
125 <output name="Biolegio plate" file="biolegio_plate_muconate.csv" ftype="csv" compare="diff"/> 124 <output name="Biolegio_plate" file="biolegio_plate_muconate.csv" ftype="csv" compare="diff"/>
126 </test> 125 </test>
127 </tests> 126 </tests>
128 <help><![CDATA[ 127 <help><![CDATA[
129 rpbasicdesign 128 rpbasicdesign
130 ================ 129 ================
131 130
132 Convert rpSBML enzyme info in to BASIC construct. UniProt IDs corresponding 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.
133 enzyme variants are extracted rpSBMl files. Promoters and RBSs are randomly
134 chosen from a default list. CDSs, in other words gene variants, of enzymes are
135 randomly chosen from amongst the UniProt IDs extracted. Constructs generated
136 can be stored as (i) a CSV file ready to be used by DNA-Bot, (ii) as SBOL
137 files.
138 132
139 Input 133 Input
140 ----- 134 -----
141 135
142 Required: 136 Required:
143 137
144 * **rpsbml_file**\ : (string) rpSBML file from which enzymes UniProt IDs will be collected. 138 * **rpSBML file**\ : rpSBML file from which enzymes UniProt IDs will be collected.
145 139
146 Advanced options: 140 Advanced options:
147 141
148 * **parts_files**\ : (string) List of files providing available linkers and user parts (backbone, promoters, ...) for constructs. Default: [data/biolegio_parts.csv, data/user_parts.csv] 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).
149 * **lms_id**\ : (string) part ID to be used as the LMS methylated linker. Default: LMS. 143 * **LMS part ID**\ : (string) part ID to be used as the LMS methylated linker. Default: LMS.
150 * **lmp_id**\ : (string) part ID to be used as the LMP methylated linker. Default: LMP. 144 * **LMP part ID**\ : (string) part ID to be used as the LMP methylated linker. Default: LMP.
151 * **backbone_id**\ : (string) part ID to be used as the backbone. Default: BASIC_SEVA_37_CmR-p15A.1. 145 * **Backbone part ID**\ : (string) part ID to be used as the backbone. Default: BASIC_SEVA_37_CmR-p15A.1.
152 * **sample_size**\ : (int) Number of construct to generate. Default: 88. 146 * **Sample size**\ : (int) Number of construct to generate. Default: 88.
153 * **cds_permutation**\ : (boolean) Whether all combinations of CDS permutation should be built Default: true. 147 * **Perform CDS permutation?**\ : (boolean) Whether all combinations of CDS permutation should be built Default: true.
154 * **max_enz_per_rxn**\ : (integer) 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). 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).
155 149
156 Output 150 Output
157 ------ 151 ------
158 152
159 * **o_dnabot_dir**\ : (string) Output folder to write construct and plate files. It will be created if it does not exist yet. Existing files will be overwritten. Default: out/dnabot_in. 153 * **constructs**\ : CSV construct file listing the constructs to be built.
160 * **o_sbol_dir**\ : (string) Output folder to write SBOL depictions of constructs. Existing files will be overwritten. Default: not output. 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.
161 157
162 Project Links 158 Project Links
163 ------------------ 159 ------------------
164 160
165 * `GitHub <https://github.com/brsynth/rpbasicdesign>`_ 161 * `GitHub <https://github.com/brsynth/rpbasicdesign>`_