Mercurial > repos > tduigou > rpbasicdesign

annotate rpbasicdesign.xml @ 1:de9f53630349 draft

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"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"
author tduigou
date Wed, 15 Dec 2021 15:10:43 +0000
parents
children 8a087d7546b8
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1 <tool id="rpbasicdesign" name="BasicDesign" version="0.3.4">
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2 <description>Build DNA-BOT input files from rpSBML</description>
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3 <requirements>
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4 <requirement type="package" version="0.3.4">rpbasicdesign</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 python -m rpbasicdesign.cli
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8 --rpsbml_file '$rpsbml_file'
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9 #if $adv.parts_files
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10 #set files = '" "'.join([str($file) for $file in $adv.parts_files])
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11 --parts_files "${files}"
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12 #end if
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13 --lms_id '$adv.lms_id'
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14 --lmp_id '$adv.lmp_id'
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15 --backbone_id '$backbone_id'
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16 --sample_size '$sample_size'
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17 #if str($adv.cds_permutation) == "true"
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18 --cds_permutation true
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19 #else
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20 --cds_permutation false
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21 #end if
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22 --o_dnabot_dir 'out/dnabot_in'
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23 --o_sbol_dir 'out/sbol_export'
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24 ]]></command>
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25 <inputs>
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26 <param name="rpsbml_file" type="data" format="xml" label="rpSBML file"/>
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27 <param name="backbone_id" type="text" value="BASIC_SEVA_37_CmR-p15A.1" label="Backbone part ID" />
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28 <param name="sample_size" type="integer" value="88" label="Number of constructs to generate" />
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29 <section name="adv" title="Advanced Options" expanded="false">
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30 <param name="parts_files" type="data" format="csv" optional="true" multiple="true" label="Linkers and user parts" />
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31 <param name="lms_id" type="text" value="LMS" label="LMS part ID" />
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32 <param name="lmp_id" type="text" value="LMP" label="LMP part ID" />
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33 <param name="cds_permutation" type="boolean" label="Perform CDS permutation?" checked="true" />
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34 </section>
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35 </inputs>
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36 <outputs>
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37 <data name="Constructs" format="csv" from_work_dir="out/dnabot_in/constructs.csv" label="${tool.name} - ${rpsbml_file.name}: constructs" />
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38 <data name="User parts plate" format="csv" from_work_dir="out/dnabot_in/user_parts_plate.csv" label="${tool.name} - ${rpsbml_file.name}: User parts plate"/>
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39 <data name="Biolegio plate" format="csv" from_work_dir="out/dnabot_in/biolegio_plate.csv" label="${tool.name} - ${rpsbml_file.name}: Biolegio plate"/>
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40 <collection name="sbol_dir" type="list" label="${tool.name} - ${rpsbml_file.name}: SBOL constructs">
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41 <discover_datasets pattern="__designation_and_ext__" format="xml" directory="out/sbol_export" />
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42 </collection>
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43 </outputs>
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44 <tests>
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45 <test>
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46 <!-- test 1: check if identical outputs are produced -->
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47 <param name="rpsbml_file" value="lycopene_CrtEBI_from_selenzy.xml" />
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48 <param name="sample_size" value="3" />
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49 <output name="Constructs" file="constructs.csv" ftype="csv" compare="diff"/>
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50 <output name="User parts plate" file="user_parts_plate.csv" ftype="csv" compare="diff"/>
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51 <output name="Biolegio plate" file="biolegio_plate.csv" ftype="csv" compare="diff"/>
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52 <output_collection name="sbol_dir" type="list">
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53 <element name="BASIC_construct_A1" ftype="xml" value="BASIC_construct_A1.xml" sort="true"/>
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54 <element name="BASIC_construct_B1" ftype="xml" value="BASIC_construct_B1.xml" sort="true"/>
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55 <element name="BASIC_construct_C1" ftype="xml" value="BASIC_construct_C1.xml" sort="true"/>
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56 </output_collection>
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57 </test>
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58 </tests>
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59 <help><![CDATA[
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60 rpbasicdesign
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61 ================
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62
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63 Convert rpSBML enzyme info in to BASIC construct. UniProt IDs corresponding
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64 enzyme variants are extracted rpSBMl files. Promoters and RBSs are randomly
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65 chosen from a default list. CDSs, in other words gene variants, of enzymes are
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66 randomly chosen from amongst the UniProt IDs extracted. Constructs generated
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67 can be stored as (i) a CSV file ready to be used by DNA-Bot, (ii) as SBOL
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68 files.
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69
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70 Input
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71 -----
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72
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73 Required:
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74
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75 * **rpsbml_file**\ : (string) rpSBML file from which enzymes UniProt IDs will be collected.
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76
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77 Advanced options:
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78
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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]
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80 * **lms_id**\ : (string) part ID to be used as the LMS methylated linker. Default: LMS.
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81 * **lmp_id**\ : (string) part ID to be used as the LMP methylated linker. Default: LMP.
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82 * **backbone_id**\ : (string) part ID to be used as the backbone. Default: BASIC_SEVA_37_CmR-p15A.1.
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83 * **sample_size**\ : (int) Number of construct to generate.Default: 3.
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84 * **cds_permutation**\ : (boolean) Whether all combinations of CDS permutation should be built Default: true.
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85
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86 Output
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87 ------
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88
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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.
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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.
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91
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92 Project Links
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93 ------------------
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94
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95 * `GitHub <https://github.com/brsynth/rpbasicdesign>`_
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96
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97 License
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98 -------
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99
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100 * `MIT <https://github.com/brsynth/rpbasicdesign/blob/master/LICENSE.txt>`_
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101
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102 ]]></help>
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103 <citations>
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104 <citation type="bibtex">
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105 @article{10.1093/synbio/ysaa010,
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106 author = {Storch, Marko and Haines, Matthew C and Baldwin, Geoff S},
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107 title = {DNA-BOT: a low-cost, automated DNA assembly platform for synthetic biology},
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108 journal = {Synthetic Biology},
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109 volume = {5},
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parents:
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110 number = {1},
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111 year = {2020},
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tduigou
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112 month = {07},
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113 issn = {2397-7000},
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114 doi = {10.1093/synbio/ysaa010},
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115 url = {https://doi.org/10.1093/synbio/ysaa010},
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116 note = {ysaa010},
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117 eprint = {https://academic.oup.com/synbio/article-pdf/5/1/ysaa010/33722340/ysaa010.pdf},
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118 }
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119 </citation>
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120 </citations>
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121 </tool>