Mercurial > repos > tduigou > rpbasicdesign
comparison rpbasicdesign.xml @ 5:e743b6118dae draft
"planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
author | tduigou |
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date | Tue, 17 May 2022 14:50:31 +0000 |
parents | 9ba4dab7f0ba |
children | ce36e195a61b |
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1 <tool id="rpbasicdesign" name="BasicDesign" version="@TOOL_VERSION@" profile="21.09"> | 1 <tool id="rpbasicdesign" name="BasicDesign" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" 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="@VERSION_SUFFIX@">0</token> | |
4 <token name="@TOOL_VERSION@">1.1.0</token> | 5 <token name="@TOOL_VERSION@">1.1.0</token> |
5 </macros> | 6 </macros> |
6 <requirements> | 7 <requirements> |
7 <requirement type="package" version="@TOOL_VERSION@">rpbasicdesign</requirement> | 8 <requirement type="package" version="@TOOL_VERSION@">rpbasicdesign</requirement> |
8 </requirements> | 9 </requirements> |
127 </test> | 128 </test> |
128 </tests> | 129 </tests> |
129 <help><![CDATA[ | 130 <help><![CDATA[ |
130 rpbasicdesign | 131 rpbasicdesign |
131 ================ | 132 ================ |
132 | |
133 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 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. |
134 | |
135 Input | 134 Input |
136 ----- | 135 ----- |
137 | |
138 Required: | 136 Required: |
139 | |
140 * **rpSBML file**\ : rpSBML file from which enzymes UniProt IDs will be collected. | 137 * **rpSBML file**\ : rpSBML file from which enzymes UniProt IDs will be collected. |
141 | |
142 Advanced options: | 138 Advanced options: |
143 | |
144 * **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). | 139 * **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). |
145 * **LMS part ID**\ : (string) part ID to be used as the LMS methylated linker. Default: LMS. | 140 * **LMS part ID**\ : (string) part ID to be used as the LMS methylated linker. Default: LMS. |
146 * **LMP part ID**\ : (string) part ID to be used as the LMP methylated linker. Default: LMP. | 141 * **LMP part ID**\ : (string) part ID to be used as the LMP methylated linker. Default: LMP. |
147 * **Backbone part ID**\ : (string) part ID to be used as the backbone. Default: BASIC_SEVA_37_CmR-p15A.1. | 142 * **Backbone part ID**\ : (string) part ID to be used as the backbone. Default: BASIC_SEVA_37_CmR-p15A.1. |
148 * **Sample size**\ : (int) Number of construct to generate. Default: 88. | 143 * **Sample size**\ : (int) Number of construct to generate. Default: 88. |
149 * **Perform CDS permutation?**\ : (boolean) Whether all combinations of CDS permutation should be built Default: true. | 144 * **Perform CDS permutation?**\ : (boolean) Whether all combinations of CDS permutation should be built Default: true. |
150 * **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). | 145 * **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). |
151 * **Maximum number of genes per construct**\ : (int) If more genes are required, i.e. more reactions are described in the input SBML file, then the execution will failed. (Default: 3). | 146 * **Maximum number of genes per construct**\ : (int) If more genes are required, i.e. more reactions are described in the input SBML file, then the execution will failed. (Default: 3). |
152 | |
153 Output | 147 Output |
154 ------ | 148 ------ |
155 | |
156 * **constructs**\ : CSV construct file listing the constructs to be built. | 149 * **constructs**\ : CSV construct file listing the constructs to be built. |
157 * **User parts plate**\ : CSV file listing the DNA parts to be included into each construct. | 150 * **User parts plate**\ : CSV file listing the DNA parts to be included into each construct. |
158 * **Biolegio plate**\ : CSV file listing the plate coordinates of the BASIC linkers. | 151 * **Biolegio plate**\ : CSV file listing the plate coordinates of the BASIC linkers. |
159 * **SBOL constructs**\ : (optional) one SBOL (Synthetic Biology Open Language) file is produced for each construct generated in XML format. | 152 * **SBOL constructs**\ : (optional) one SBOL (Synthetic Biology Open Language) file is produced for each construct generated in XML format. |
160 | |
161 Project Links | 153 Project Links |
162 ------------------ | 154 ------------------ |
163 | |
164 * `GitHub <https://github.com/brsynth/rpbasicdesign>`_ | 155 * `GitHub <https://github.com/brsynth/rpbasicdesign>`_ |
165 | |
166 License | 156 License |
167 ------- | 157 ------- |
168 | |
169 * `MIT <https://github.com/brsynth/rpbasicdesign/blob/master/LICENSE.txt>`_ | 158 * `MIT <https://github.com/brsynth/rpbasicdesign/blob/master/LICENSE.txt>`_ |
170 | |
171 ]]></help> | 159 ]]></help> |
172 <citations> | 160 <citations> |
173 <citation type="doi">10.1093/synbio/ysaa010</citation> | 161 <citation type="doi">10.1093/synbio/ysaa010</citation> |
174 </citations> | 162 </citations> |
175 </tool> | 163 </tool> |