Mercurial > repos > iuc > rpbasicdesign
comparison rpbasicdesign.xml @ 0:cdd6a526bdcf draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rpbasicdesign commit bdac148247c9c3d3da3420220d006e723c718277"
author | iuc |
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date | Wed, 30 Mar 2022 13:05:31 +0000 |
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children | e73c927dc332 |
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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> |