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comparison rpbasicdesign.xml @ 4:9ba4dab7f0ba draft

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"planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty"
author tduigou
date Fri, 06 May 2022 16:26:26 +0000
parents e4821c820f7c
children e743b6118dae
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3:e4821c820f7c 4:9ba4dab7f0ba
1 <tool id="rpbasicdesign" name="BasicDesign" version="@TOOL_VERSION@" profile="21.09"> 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@">1.1.0</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">rpbasicdesign</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">rpbasicdesign</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
19 --sample_size '$sample_size' 19 --sample_size '$sample_size'
20 $adv.cds_permutation 20 $adv.cds_permutation
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 --max_gene_per_construct $adv.max_gene_per_construct
24 ]]></command> 25 ]]></command>
25 <inputs> 26 <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 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 <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 <sanitizer invalid_char="">
61 <validator type="empty_field" message="LMP ID is required"/> 62 <validator type="empty_field" message="LMP ID is required"/>
62 </param> 63 </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="--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="--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 <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 <param argument="--max_gene_per_construct" type="integer" value="3" min="1" max="10" label="Maximum number of genes per construct" help="If more genes are required, i.e. more reactions are described in the input SBML file, then the execution will failed."/>
66 </section> 68 </section>
67 </inputs> 69 </inputs>
68 <outputs> 70 <outputs>
69 <data name="Constructs" format="csv" from_work_dir="out/dnabot_in/constructs.csv" label="${tool.name} on ${rpsbml_file.name}: constructs" /> 71 <data name="Constructs" format="csv" from_work_dir="out/dnabot_in/constructs.csv" label="${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 ${rpsbml_file.name}: User parts plate"/> 72 <data name="User_parts_plate" format="csv" from_work_dir="out/dnabot_in/user_parts_plate.csv" label="${tool.name} on ${rpsbml_file.name}: User parts plate"/>
143 * **LMS part ID**\ : (string) part ID to be used as the LMS methylated linker. Default: LMS. 145 * **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. 146 * **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. 147 * **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 construct to generate. Default: 88. 148 * **Sample size**\ : (int) Number of construct to generate. Default: 88.
147 * **Perform CDS permutation?**\ : (boolean) Whether all combinations of CDS permutation should be built Default: true. 149 * **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). 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).
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).
149 152
150 Output 153 Output
151 ------ 154 ------
152 155
153 * **constructs**\ : CSV construct file listing the constructs to be built. 156 * **constructs**\ : CSV construct file listing the constructs to be built.