Mercurial > repos > tduigou > rpbasicdesign

annotate 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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1 <tool id="rpbasicdesign" name="BasicDesign" version="@TOOL_VERSION@" profile="21.09">
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2 <description>Build DNA-BOT input files from rpSBML</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.1.0</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">rpbasicdesign</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 python -m rpbasicdesign.cli
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11 --rpsbml_file '$rpsbml_file'
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12 #if $adv.parts_files
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13 #set files = '" "'.join([str($file) for $file in $adv.parts_files])
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14 --parts_files "${files}"
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15 #end if
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16 --lms_id '$adv.lms_id'
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17 --lmp_id '$adv.lmp_id'
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18 --backbone_id '$backbone_id'
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19 --sample_size '$sample_size'
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20 $adv.cds_permutation
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21 --o_dnabot_dir 'out/dnabot_in'
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22 $adv.sbol_output
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23 --max_enz_per_rxn $adv.max_enz_per_rxn
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24 --max_gene_per_construct $adv.max_gene_per_construct
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25 ]]></command>
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26 <inputs>
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27 <param name="rpsbml_file" type="data" format="sbml" label="rpSBML file" help="SBML file from which enzymes UniProt IDs will be collected."/>
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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.">
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29 <sanitizer invalid_char="">
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30 <valid initial="string.letters,string.digits">
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31 <add value=":" />
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32 <add value="." />
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33 <add value="-" />
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34 <add value="_" />
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35 </valid>
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36 </sanitizer>
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37 <validator type="empty_field" message="Backbone ID is required"/>
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38 </param>
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39 <param argument="--sample_size" type="integer" value="88" min="1" max="88" label="Sample size" help="Number of construct to generate."/>
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40 <section name="adv" title="Advanced Options" expanded="false">
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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 (BBP-18500)" />
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42 <param argument="--lms_id" type="text" value="LMS" label="LMS part ID" help="Part ID to be used as the LMS methylated linker." >
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43 <sanitizer invalid_char="">
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44 <valid initial="string.letters,string.digits">
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45 <add value=":" />
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46 <add value="-" />
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47 <add value="_" />
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48 <add value="." />
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49 </valid>
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50 </sanitizer>
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51 <validator type="empty_field" message="LMS ID is required"/>
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52 </param>
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53 <param argument="--lmp_id" type="text" value="LMP" label="LMP part ID" help="Part ID to be used as the LMP methylated linker.">
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54 <sanitizer invalid_char="">
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55 <valid initial="string.letters,string.digits">
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56 <add value=":" />
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57 <add value="-" />
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58 <add value="_" />
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59 <add value="." />
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60 </valid>
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61 </sanitizer>
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62 <validator type="empty_field" message="LMP ID is required"/>
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63 </param>
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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." />
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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" />
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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."/>
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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."/>
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68 </section>
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69 </inputs>
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70 <outputs>
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71 <data name="Constructs" format="csv" from_work_dir="out/dnabot_in/constructs.csv" label="${tool.name} on ${rpsbml_file.name}: constructs" />
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72 <data name="User_parts_plate" format="csv" from_work_dir="out/dnabot_in/user_parts_plate.csv" label="${tool.name} on ${rpsbml_file.name}: User parts plate"/>
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73 <data name="Biolegio_plate" format="csv" from_work_dir="out/dnabot_in/biolegio_plate.csv" label="${tool.name} on ${rpsbml_file.name}: Biolegio plate"/>
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74 <collection name="sbol_dir" type="list" label="${tool.name} on ${rpsbml_file.name}: SBOL constructs">
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75 <filter> adv['sbol_output'] </filter>
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76 <discover_datasets pattern="__designation_and_ext__" format="xml" directory="out/sbol_export" />
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77 </collection>
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78 </outputs>
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79 <tests>
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80 <test expect_num_outputs="4">
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81 <!-- test 1: check if identical outputs are produced (Lycopene input)-->
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82 <param name="rpsbml_file" value="lycopene_CrtEBI_from_selenzy.xml" />
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83 <param name="sample_size" value="3" />
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84 <output name="Constructs" file="constructs_lycopene.csv" ftype="csv" compare="diff">
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85 <assert_contents>
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86 <has_n_lines n="4"/>
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87 </assert_contents>
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88 </output>
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89 <output name="User_parts_plate" file="user_parts_plate_lycopene.csv" ftype="csv" compare="diff"/>
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90 <output name="Biolegio_plate" file="biolegio_plate_lycopene.csv" ftype="csv" compare="diff"/>
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91 <param name="sbol_output" value="true" />
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92 <output_collection name="sbol_dir" type="list" count="3">
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93 <element name="BASIC_construct_A1">
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94 <assert_contents>
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95 <is_valid_xml />
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96 <has_text text="BASIC_construct_A1" />
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97 <has_n_lines n="339" />
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98 </assert_contents>
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99 </element>
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100 <element name="BASIC_construct_B1">
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101 <assert_contents>
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102 <is_valid_xml />
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103 <has_text text="BASIC_construct_B1" />
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104 <has_n_lines n="339" />
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105 </assert_contents>
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106 </element>
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107 <element name="BASIC_construct_C1">
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108 <assert_contents>
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109 <is_valid_xml />
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110 <has_text text="BASIC_construct_C1" />
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111 <has_n_lines n="339" />
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112 </assert_contents>
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113 </element>
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114 </output_collection>
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115 </test>
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116 <test expect_num_outputs="3">
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117 <!-- test 2: check if identical outputs are produced (Muconate input)-->
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118 <param name="rpsbml_file" value="muconate_example.xml" />
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119 <param name="sample_size" value="88" />
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120 <output name="Constructs" file="constructs_muconate.csv" ftype="csv" compare="diff">
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121 <assert_contents>
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122 <has_n_lines n="89"/>
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123 </assert_contents>
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124 </output>
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125 <output name="User_parts_plate" file="user_parts_plate_muconate.csv" ftype="csv" compare="diff"/>
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126 <output name="Biolegio_plate" file="biolegio_plate_muconate.csv" ftype="csv" compare="diff"/>
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127 </test>
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128 </tests>
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129 <help><![CDATA[
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130 rpbasicdesign
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131 ================
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132
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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.
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134
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135 Input
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136 -----
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137
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138 Required:
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139
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140 * **rpSBML file**\ : rpSBML file from which enzymes UniProt IDs will be collected.
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141
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142 Advanced options:
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143
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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).
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145 * **LMS part ID**\ : (string) part ID to be used as the LMS methylated linker. Default: LMS.
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146 * **LMP part ID**\ : (string) part ID to be used as the LMP methylated linker. Default: LMP.
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147 * **Backbone part ID**\ : (string) part ID to be used as the backbone. Default: BASIC_SEVA_37_CmR-p15A.1.
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148 * **Sample size**\ : (int) Number of construct to generate. Default: 88.
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149 * **Perform CDS permutation?**\ : (boolean) Whether all combinations of CDS permutation should be built Default: true.
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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).
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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).
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152
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153 Output
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154 ------
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155
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156 * **constructs**\ : CSV construct file listing the constructs to be built.
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157 * **User parts plate**\ : CSV file listing the DNA parts to be included into each construct.
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158 * **Biolegio plate**\ : CSV file listing the plate coordinates of the BASIC linkers.
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159 * **SBOL constructs**\ : (optional) one SBOL (Synthetic Biology Open Language) file is produced for each construct generated in XML format.
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160
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161 Project Links
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162 ------------------
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163
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164 * `GitHub <https://github.com/brsynth/rpbasicdesign>`_
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165
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166 License
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167 -------
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168
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169 * `MIT <https://github.com/brsynth/rpbasicdesign/blob/master/LICENSE.txt>`_
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170
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171 ]]></help>
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172 <citations>
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173 <citation type="doi">10.1093/synbio/ysaa010</citation>
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174 </citations>
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175 </tool>