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comparison rpbasicdesign.xml @ 4:f1c4341fc13a draft

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"planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
author tduigou
date Mon, 28 Mar 2022 14:16:02 +0000
parents 4bcc0e048d93
children 2bdbcdb151ac
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3:4bcc0e048d93 4:f1c4341fc13a
1 <tool id="rpbasicdesign" name="BasicDesign" version="0.3.4"> 1 <tool id="rpbasicdesign" name="BasicDesign" version="@TOOL_VERSION@" profile="19.09">
2 <description>Build DNA-BOT input files from rpSBML</description> 2 <description>Build DNA-BOT input files from rpSBML</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.0.1</token>
5 </macros>
3 <requirements> 6 <requirements>
4 <requirement type="package" version="0.3.4">rpbasicdesign</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">rpbasicdesign</requirement>
5 </requirements> 8 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
7 python -m rpbasicdesign.cli 10 python -m rpbasicdesign.cli
8 --rpsbml_file '$rpsbml_file' 11 --rpsbml_file '$rpsbml_file'
9 #if $adv.parts_files 12 #if $adv.parts_files
12 #end if 15 #end if
13 --lms_id '$adv.lms_id' 16 --lms_id '$adv.lms_id'
14 --lmp_id '$adv.lmp_id' 17 --lmp_id '$adv.lmp_id'
15 --backbone_id '$backbone_id' 18 --backbone_id '$backbone_id'
16 --sample_size '$sample_size' 19 --sample_size '$sample_size'
17 #if str($adv.cds_permutation) == "true" 20 $adv.cds_permutation
18 --cds_permutation true
19 #else
20 --cds_permutation false
21 #end if
22 --o_dnabot_dir 'out/dnabot_in' 21 --o_dnabot_dir 'out/dnabot_in'
23 --o_sbol_dir 'out/sbol_export' 22 $adv.sbol_output
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"/> 26 <param name="rpsbml_file" type="data" format="xml" label="rpSBML file" help="SBML file from which enzymes UniProt IDs will be collected."/>
27 <param name="backbone_id" type="text" value="BASIC_SEVA_37_CmR-p15A.1" label="Backbone part ID" /> 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 <param name="sample_size" type="integer" value="88" label="Number of constructs to generate" /> 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 <validator type="regex">[0-9a-zA-Z_:-]+</validator>
38 </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."/>
29 <section name="adv" title="Advanced Options" expanded="false"> 40 <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" /> 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" />
31 <param name="lms_id" type="text" value="LMS" label="LMS part ID" /> 42 <param argument="--lms_id" type="text" value="LMS" label="LMS part ID" help="Part ID to be used as the LMS methylated linker." >
32 <param name="lmp_id" type="text" value="LMP" label="LMP part ID" /> 43 <sanitizer invalid_char="">
33 <param name="cds_permutation" type="boolean" label="Perform CDS permutation?" checked="true" /> 44 <valid initial="string.letters,string.digits">
45 <add value=":" />
46 <add value="-" />
47 <add value="_" />
48 <add value="." />
49 </valid>
50 </sanitizer>
51 <validator type="empty_field" message="LMS ID is required"/>
52 </param>
53 <param argument="--lmp_id" type="text" value="LMP" label="LMP part ID" help="Part ID to be used as the LMP methylated linker.">
54 <sanitizer invalid_char="">
55 <valid initial="string.letters,string.digits">
56 <add value=":" />
57 <add value="-" />
58 <add value="_" />
59 <add value="." />
60 </valid>
61 </sanitizer>
62 <validator type="empty_field" message="LMP ID is required"/>
63 </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." />
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." />
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."/>
34 </section> 67 </section>
35 </inputs> 68 </inputs>
36 <outputs> 69 <outputs>
37 <data name="Constructs" format="csv" from_work_dir="out/dnabot_in/constructs.csv" label="${tool.name} - ${rpsbml_file.name}: constructs" /> 70 <data name="Constructs" format="csv" from_work_dir="out/dnabot_in/constructs.csv" label="${tool.name} on ${rpsbml_file.name}: constructs" />
38 <data name="User parts plate" format="csv" from_work_dir="out/dnabot_in/user_parts_plate.csv" label="${tool.name} - ${rpsbml_file.name}: User parts plate"/> 71 <data name="User parts plate" format="csv" from_work_dir="out/dnabot_in/user_parts_plate.csv" label="${tool.name} on ${rpsbml_file.name}: User parts plate"/>
39 <data name="Biolegio plate" format="csv" from_work_dir="out/dnabot_in/biolegio_plate.csv" label="${tool.name} - ${rpsbml_file.name}: Biolegio plate"/> 72 <data name="Biolegio plate" format="csv" from_work_dir="out/dnabot_in/biolegio_plate.csv" label="${tool.name} on ${rpsbml_file.name}: Biolegio plate"/>
40 <collection name="sbol_dir" type="list" label="${tool.name} - ${rpsbml_file.name}: SBOL constructs"> 73 <collection name="sbol_dir" type="list" label="${tool.name} on ${rpsbml_file.name}: SBOL constructs">
74 <filter> adv['sbol_output'] </filter>
41 <discover_datasets pattern="__designation_and_ext__" format="xml" directory="out/sbol_export" /> 75 <discover_datasets pattern="__designation_and_ext__" format="xml" directory="out/sbol_export" />
42 </collection> 76 </collection>
43 </outputs> 77 </outputs>
44 <tests> 78 <tests>
45 <test> 79 <test>
46 <!-- test 1: check if identical outputs are produced --> 80 <!-- test 1: check if identical outputs are produced (Lycopene input)-->
47 <param name="rpsbml_file" value="lycopene_CrtEBI_from_selenzy.xml" /> 81 <param name="rpsbml_file" value="lycopene_CrtEBI_from_selenzy.xml" />
48 <param name="sample_size" value="3" /> 82 <param name="sample_size" value="3" />
49 <output name="Constructs" file="constructs.csv" ftype="csv" compare="diff"/> 83 <output name="Constructs" file="constructs_lycopene.csv" ftype="csv" compare="diff">
50 <output name="User parts plate" file="user_parts_plate.csv" ftype="csv" compare="diff"/> 84 <assert_contents>
51 <output name="Biolegio plate" file="biolegio_plate.csv" ftype="csv" compare="diff"/> 85 <has_n_lines n="4"/>
52 <output_collection name="sbol_dir" type="list"> 86 </assert_contents>
53 <element name="BASIC_construct_A1" ftype="xml" value="BASIC_construct_A1.xml" sort="true"/> 87 </output>
54 <element name="BASIC_construct_B1" ftype="xml" value="BASIC_construct_B1.xml" sort="true"/> 88 <output name="User parts plate" file="user_parts_plate_lycopene.csv" ftype="csv" compare="diff"/>
55 <element name="BASIC_construct_C1" ftype="xml" value="BASIC_construct_C1.xml" sort="true"/> 89 <output name="Biolegio plate" file="biolegio_plate_lycopene.csv" ftype="csv" compare="diff"/>
56 </output_collection> 90 <param name="sbol_output" value="--o_sbol_dir out/sbol_export" />
91 <output_collection name="sbol_dir" type="list" count="3">
92 <element name="BASIC_construct_A1">
93 <assert_contents>
94 <is_valid_xml />
95 <has_text text="BASIC_construct_A1" />
96 <has_n_lines n="339" />
97 </assert_contents>
98 </element>
99 <element name="BASIC_construct_B1">
100 <assert_contents>
101 <is_valid_xml />
102 <has_text text="BASIC_construct_B1" />
103 <has_n_lines n="339" />
104 </assert_contents>
105 </element>
106 <element name="BASIC_construct_C1">
107 <assert_contents>
108 <is_valid_xml />
109 <has_text text="BASIC_construct_C1" />
110 <has_n_lines n="339" />
111 </assert_contents>
112 </element>
113 </output_collection>
114 </test>
115 <test>
116 <!-- test 2: check if identical outputs are produced (Muconate input)-->
117 <param name="rpsbml_file" value="muconate_example.xml" />
118 <param name="sample_size" value="88" />
119 <output name="Constructs" file="constructs_muconate.csv" ftype="csv" compare="diff">
120 <assert_contents>
121 <has_n_lines n="89"/>
122 </assert_contents>
123 </output>
124 <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"/>
57 </test> 126 </test>
58 </tests> 127 </tests>
59 <help><![CDATA[ 128 <help><![CDATA[
60 rpbasicdesign 129 rpbasicdesign
61 ================ 130 ================
74 143
75 * **rpsbml_file**\ : (string) rpSBML file from which enzymes UniProt IDs will be collected. 144 * **rpsbml_file**\ : (string) rpSBML file from which enzymes UniProt IDs will be collected.
76 145
77 Advanced options: 146 Advanced options:
78 147
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] 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]
80 * **lms_id**\ : (string) part ID to be used as the LMS methylated linker. Default: LMS. 149 * **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. 150 * **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. 151 * **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. 152 * **sample_size**\ : (int) Number of construct to generate. Default: 88.
84 * **cds_permutation**\ : (boolean) Whether all combinations of CDS permutation should be built Default: true. 153 * **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).
85 155
86 Output 156 Output
87 ------ 157 ------
88 158
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. 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.
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. 160 * **o_sbol_dir**\ : (string) Output folder to write SBOL depictions of constructs. Existing files will be overwritten. Default: not output.
91 161
92 Project Links 162 Project Links
93 ------------------ 163 ------------------
94 164
95 * `GitHub <https://github.com/brsynth/rpbasicdesign>`_ 165 * `GitHub <https://github.com/brsynth/rpbasicdesign>`_
99 169
100 * `MIT <https://github.com/brsynth/rpbasicdesign/blob/master/LICENSE.txt>`_ 170 * `MIT <https://github.com/brsynth/rpbasicdesign/blob/master/LICENSE.txt>`_
101 171
102 ]]></help> 172 ]]></help>
103 <citations> 173 <citations>
104 <citation type="bibtex"> 174 <citation type="doi">10.1093/synbio/ysaa010</citation>
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> 175 </citations>
121 </tool> 176 </tool>