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comparison rpbasicdesign.xml @ 1:de9f53630349 draft

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author tduigou
date Wed, 15 Dec 2021 15:10:43 +0000
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1 <tool id="rpbasicdesign" name="BasicDesign" version="0.3.4">
2 <description>Build DNA-BOT input files from rpSBML</description>
3 <requirements>
4 <requirement type="package" version="0.3.4">rpbasicdesign</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 python -m rpbasicdesign.cli
8 --rpsbml_file '$rpsbml_file'
9 #if $adv.parts_files
10 #set files = '" "'.join([str($file) for $file in $adv.parts_files])
11 --parts_files "${files}"
12 #end if
13 --lms_id '$adv.lms_id'
14 --lmp_id '$adv.lmp_id'
15 --backbone_id '$backbone_id'
16 --sample_size '$sample_size'
17 #if str($adv.cds_permutation) == "true"
18 --cds_permutation true
19 #else
20 --cds_permutation false
21 #end if
22 --o_dnabot_dir 'out/dnabot_in'
23 --o_sbol_dir 'out/sbol_export'
24 ]]></command>
25 <inputs>
26 <param name="rpsbml_file" type="data" format="xml" label="rpSBML file"/>
27 <param name="backbone_id" type="text" value="BASIC_SEVA_37_CmR-p15A.1" label="Backbone part ID" />
28 <param name="sample_size" type="integer" value="88" label="Number of constructs to generate" />
29 <section name="adv" title="Advanced Options" expanded="false">
30 <param name="parts_files" type="data" format="csv" optional="true" multiple="true" label="Linkers and user parts" />
31 <param name="lms_id" type="text" value="LMS" label="LMS part ID" />
32 <param name="lmp_id" type="text" value="LMP" label="LMP part ID" />
33 <param name="cds_permutation" type="boolean" label="Perform CDS permutation?" checked="true" />
34 </section>
35 </inputs>
36 <outputs>
37 <data name="Constructs" format="csv" from_work_dir="out/dnabot_in/constructs.csv" label="${tool.name} - ${rpsbml_file.name}: constructs" />
38 <data name="User parts plate" format="csv" from_work_dir="out/dnabot_in/user_parts_plate.csv" label="${tool.name} - ${rpsbml_file.name}: User parts plate"/>
39 <data name="Biolegio plate" format="csv" from_work_dir="out/dnabot_in/biolegio_plate.csv" label="${tool.name} - ${rpsbml_file.name}: Biolegio plate"/>
40 <collection name="sbol_dir" type="list" label="${tool.name} - ${rpsbml_file.name}: SBOL constructs">
41 <discover_datasets pattern="__designation_and_ext__" format="xml" directory="out/sbol_export" />
42 </collection>
43 </outputs>
44 <tests>
45 <test>
46 <!-- test 1: check if identical outputs are produced -->
47 <param name="rpsbml_file" value="lycopene_CrtEBI_from_selenzy.xml" />
48 <param name="sample_size" value="3" />
49 <output name="Constructs" file="constructs.csv" ftype="csv" compare="diff"/>
50 <output name="User parts plate" file="user_parts_plate.csv" ftype="csv" compare="diff"/>
51 <output name="Biolegio plate" file="biolegio_plate.csv" ftype="csv" compare="diff"/>
52 <output_collection name="sbol_dir" type="list">
53 <element name="BASIC_construct_A1" ftype="xml" value="BASIC_construct_A1.xml" sort="true"/>
54 <element name="BASIC_construct_B1" ftype="xml" value="BASIC_construct_B1.xml" sort="true"/>
55 <element name="BASIC_construct_C1" ftype="xml" value="BASIC_construct_C1.xml" sort="true"/>
56 </output_collection>
57 </test>
58 </tests>
59 <help><![CDATA[
60 rpbasicdesign
61 ================
62
63 Convert rpSBML enzyme info in to BASIC construct. UniProt IDs corresponding
64 enzyme variants are extracted rpSBMl files. Promoters and RBSs are randomly
65 chosen from a default list. CDSs, in other words gene variants, of enzymes are
66 randomly chosen from amongst the UniProt IDs extracted. Constructs generated
67 can be stored as (i) a CSV file ready to be used by DNA-Bot, (ii) as SBOL
68 files.
69
70 Input
71 -----
72
73 Required:
74
75 * **rpsbml_file**\ : (string) rpSBML file from which enzymes UniProt IDs will be collected.
76
77 Advanced options:
78
79 * **parts_files**\ : (string) List of files providing available linkers and user parts (backbone, promoters, ...) for constructs. Default: [data/biolegio_parts.csv, user_parts.csv]
80 * **lms_id**\ : (string) part ID to be used as the LMS methylated linker. Default: LMS.
81 * **lmp_id**\ : (string) part ID to be used as the LMP methylated linker. Default: LMP.
82 * **backbone_id**\ : (string) part ID to be used as the backbone. Default: BASIC_SEVA_37_CmR-p15A.1.
83 * **sample_size**\ : (int) Number of construct to generate.Default: 3.
84 * **cds_permutation**\ : (boolean) Whether all combinations of CDS permutation should be built Default: true.
85
86 Output
87 ------
88
89 * **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.
90 * **o_sbol_dir**\ : (string) Output folder to write SBOL depictions of constructs. It will be created if it does not exist yet. Existing files will be overwritten. Default: out/sbol_export.
91
92 Project Links
93 ------------------
94
95 * `GitHub <https://github.com/brsynth/rpbasicdesign>`_
96
97 License
98 -------
99
100 * `MIT <https://github.com/brsynth/rpbasicdesign/blob/master/LICENSE.txt>`_
101
102 ]]></help>
103 <citations>
104 <citation type="bibtex">
105 @article{10.1093/synbio/ysaa010,
106 author = {Storch, Marko and Haines, Matthew C and Baldwin, Geoff S},
107 title = {DNA-BOT: a low-cost, automated DNA assembly platform for synthetic biology},
108 journal = {Synthetic Biology},
109 volume = {5},
110 number = {1},
111 year = {2020},
112 month = {07},
113 issn = {2397-7000},
114 doi = {10.1093/synbio/ysaa010},
115 url = {https://doi.org/10.1093/synbio/ysaa010},
116 note = {ysaa010},
117 eprint = {https://academic.oup.com/synbio/article-pdf/5/1/ysaa010/33722340/ysaa010.pdf},
118 }
119 </citation>
120 </citations>
121 </tool>