Mercurial > repos > tduigou > create_assembly_picklists

annotate create_assembly_picklists.xml @ 2:868cf39d9b15 draft

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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit fe52aec22c97cd357d1b6c40c2954d27ebad87d3-dirty
author tduigou
date Wed, 06 Aug 2025 14:41:58 +0000
parents 196e13c09881
children 9f9bb8d0dd4e
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4bde3e90ee98 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Plateo commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty
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1 <tool id="create_assembly_picklists" name="Create Assembly Picklists" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
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2 <description>Provide a source plate map and an assembly plan, get a robotic picklist spreadsheet for Tecan EVO or Labcyte Echo</description>
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3 <macros>
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4 <token name="@VERSION_SUFFIX@">0</token>
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5 <token name="@TOOL_VERSION@">0.1.0</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="0.18.0">fuzzywuzzy</requirement>
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9 <requirement type="package" version="0.3.4">bandwagon</requirement>
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10 <requirement type="package" version="1.85">biopython</requirement>
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11 <requirement type="package" version="0.2.2">crazydoc</requirement>
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12 <requirement type="package" version="2.0.12">dnacauldron</requirement>
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13 <requirement type="package" version="3.2.16">dnachisel</requirement>
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14 <requirement type="package" version="0.1.11">flametree</requirement>
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15 <requirement type="package" version="0.3.1">plateo</requirement>
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16 <requirement type="package" version="0.1.23">snapgene-reader</requirement>
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17 </requirements>
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18 <command detect_errors="exit_code"><![CDATA[
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19 #set genbank_file_paths = ','.join([str(f) for f in $genbank_files])
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20 #set file_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $genbank_files])
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22 #set backbone_list = [line.strip() for line in str($backbone_name).strip().split('\n') if line.strip()]
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23 #set backbone_name = ','.join(backbone_list)
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25 mkdir renamed_parts &&
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26 touch 'picklist.zip' &&
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27 touch 'source_plate.xlsx' &&
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29 #for $file in $genbank_files
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30 cp '$file.file_name' 'renamed_parts/$file.name' &&
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31 #end for
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33 #set renamed_paths = ','.join(['renamed_parts/%s' % file.name for file in $genbank_files])
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34
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35 cp '$source_plate' 'source_plate.xlsx' &&
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36
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37 python '$__tool_directory__/CreateAssemblyPicklists_script.py'
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38 --parts_files '$renamed_paths'
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39 --picklist '$picklist'
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40 --source_plate 'source_plate.xlsx'
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41 --backbone_name '$adv.backbone_name'
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42 --part_backbone_ratio '$adv.part_backbone_ratio'
0
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43 --quantity_unit '$quantity_unit'
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44 --part_quantity '$part_quantity'
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45 --buffer_volume '$buffer_volume'
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46 --total_volume '$total_volume'
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47 --dispenser '$dispenser'
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48 --result_zip 'picklist.zip' &&
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49 cp 'picklist.zip' '$output_zip'
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50 ]]></command>
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51 <inputs>
1
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52 <param name="genbank_files" type="data_collection" collection_type="list" format="genbank,fasta" label="GenBank and/or Fasta File(s)" />
0
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53 <param name="picklist" type="data" format="xlsx,xls,csv" label="Assembly Plan (csv or excel)"/>
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54 <param name="source_plate" type="data" format="xlsx,xls" label="Source Plate (excel)"/>
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55 <param name="quantity_unit" type="select" label="Part quantity unit">
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56 <option value="fmol" selected="true">femto-mole</option>
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57 <option value="nM">nano-molar</option>
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58 <option value="ng">nano-gram</option>
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59 </param>
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60 <param name="part_quantity" type="float" value="1.3" label="Part quantity" />
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61 <param name="buffer_volume" type="float" value="0.3" label="Buffer volume (µL)" />
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62 <param name="total_volume" type="float" value="1.0" label="Total volume (µL)" />
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63 <param name="dispenser" type="select" label="Dispenser Machine">
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64 <option value="labcyte_echo" selected="true">Labcyte ECHO</option>
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65 <option value="tecan_evo">Tecab EVO</option>
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66 </param>
1
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67 <section name="adv" title="advance" expanded="false">
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68 <param name="backbone_name" type="text" area="True" label="Backbone Name(s)" optional='true'/>
2
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69 <param name="part_backbone_ratio" type="float" value='1.0' min="0" max="1.0" label="Backbone Molar Ratio" optional='true' />
1
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70 </section>
0
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71 </inputs>
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72 <outputs>
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73 <data format="zip" name="output_zip" label="picklist (zip)"/>
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74 </outputs>
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75 <tests>
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76 <!--test type2s_assembly class-->
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77 <!--python CreateAssemblyPicklists_script.py parts_files "test-data/emma_parts/HC_Amp_ccdB.gb,test-data/emma_parts/conn a-c.gb,test-data/emma_parts/conn b-e.gb,test-data/emma_parts/conn b-l.gb,test-data/emma_parts/conn d-e.gb,test-data/emma_parts/conn d-f.gb,test-data/emma_parts/conn h-ha.gb,test-data/emma_parts/conn h-j.gb,test-data/emma_parts/conn h-k.gb,test-data/emma_parts/conn j-k.gb,test-data/emma_parts/conn l-n.gb,test-data/emma_parts/conn l-r.gb,test-data/emma_parts/conn l-w.gb,test-data/emma_parts/conn l-y.gb,test-data/emma_parts/conn q-r.gb,test-data/emma_parts/conn r-w.gb,test-data/emma_parts/conn t-v.gb,test-data/emma_parts/conn w-x.gb,test-data/emma_parts/conn w-y.gb,test-data/emma_parts/conn w-z.gb,test-data/emma_parts/conn y-z.gb,test-data/emma_parts/p10_tet-aptazyme.gb,test-data/emma_parts/p11_sv40polya.gb,test-data/emma_parts/p14_cmvp.gb,test-data/emma_parts/p14_sv40p.gb,test-data/emma_parts/p15_puror.gb,test-data/emma_parts/p16_bghpolya.gb,test-data/emma_parts/p18_cmvp.gb,test-data/emma_parts/p18_ef1ap.gb,test-data/emma_parts/p19_mneogreen.gb,test-data/emma_parts/p19_mruby2.gb,test-data/emma_parts/p19_mtagbfp2.gb,test-data/emma_parts/p19_tet-on-3g.gb,test-data/emma_parts/p1_5'-itr-pb.gb,test-data/emma_parts/p1_5'ha-haavs1.gb,test-data/emma_parts/p20_ct-minute-nes.gb,test-data/emma_parts/p20_ct-nes.gb,test-data/emma_parts/p20_linker3.gb,test-data/emma_parts/p20_p2a.gb,test-data/emma_parts/p21_dmra.gb,test-data/emma_parts/p21_mkate2.gb,test-data/emma_parts/p21_mneogreen.gb,test-data/emma_parts/p21_mruby2.gb,test-data/emma_parts/p21_mtagbfp2.gb,test-data/emma_parts/p21_puror.gb,test-data/emma_parts/p22_pgkpolya.gb,test-data/emma_parts/p23_insulatorfb.gb,test-data/emma_parts/p24_3'ha_haavs1.gb,test-data/emma_parts/p24_3'pb.gb,test-data/emma_parts/p25_sv40-ori.gb,test-data/emma_parts/p2_insulatorfb.gb,test-data/emma_parts/p3_cagp.gb,test-data/emma_parts/p3_cmvp_tet.gb,test-data/emma_parts/p3_ef1ap.gb,test-data/emma_parts/p3_tre3gp.gb,test-data/emma_parts/p4_kt-l7ae -weiss.gb,test-data/emma_parts/p4_lac-o.gb,test-data/emma_parts/p5_attb-bxb1.gb,test-data/emma_parts/p5_attp-bxb1.gb,test-data/emma_parts/p5_k1-k1.gb,test-data/emma_parts/p5_kt-weiss.gb,test-data/emma_parts/p6_atg_boxc.gb,test-data/emma_parts/p6_kozak-atg.gb,test-data/emma_parts/p6_nt-igkl sequence.gb,test-data/emma_parts/p6_nt-mls.gb,test-data/emma_parts/p6_nt-myristoylation signal.gb,test-data/emma_parts/p6_nt-palm sequence.gb,test-data/emma_parts/p6_nt-sv40_nls.gb,test-data/emma_parts/p7_bxb1.gb,test-data/emma_parts/p7_l7ae-weiss.gb,test-data/emma_parts/p7_l7ae.gb,test-data/emma_parts/p7_laci.gb,test-data/emma_parts/p7_mcherry.gb,test-data/emma_parts/p7_mkate2.gb,test-data/emma_parts/p7_mneogreen.gb,test-data/emma_parts/p7_mruby2.gb,test-data/emma_parts/p7_mtagbfp2.gb,test-data/emma_parts/p8_linker1.gb,test-data/emma_parts/p8_linker2.gb,test-data/emma_parts/p8_p2a.gb,test-data/emma_parts/p8a_ct-kdel.gb,test-data/emma_parts/p8b_ires2.gb,test-data/emma_parts/p9_a-tubulin.gb,test-data/emma_parts/p9_bsdr.gb,test-data/emma_parts/p9_dmrc.gb,test-data/emma_parts/p9_firefly luciferase.gb,test-data/emma_parts/p9_mneogreen.gb,test-data/emma_parts/p9_mruby2.gb,test-data/emma_parts/p9_mtagbfp2.gb,test-data/emma_parts/p9_neor.gb,test-data/emma_parts/p9_puror.gb" backbone_name 'HC_Amp_ccdb' part_backbone_ratio '1.0' quantity_unit 'fmol' part_quantity '1.3' buffer_volume '0.3' total_volume '1.0' dispenser 'labcyte_echo' result_zip 'picklist.zip' picklist 'test-data/example_picklist.xls' source_plate 'test-data/example_echo_plate.xlsx'-->
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78 <test>
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79 <param name="genbank_files">
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80 <collection type="list">
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81 <element name="HC_Amp_ccdB" value="emma_parts/HC_Amp_ccdB.gb" />
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82 <element name="conn a-c" value="emma_parts/conn a-c.gb" />
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83 <element name="conn b-e" value="emma_parts/conn b-e.gb" />
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84 <element name="conn b-l" value="emma_parts/conn b-l.gb" />
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85 <element name="conn d-e" value="emma_parts/conn d-e.gb" />
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86 <element name="conn d-f" value="emma_parts/conn d-f.gb" />
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87 <element name="conn h-ha" value="emma_parts/conn h-ha.gb" />
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88 <element name="conn h-j" value="emma_parts/conn h-j.gb" />
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89 <element name="conn h-k" value="emma_parts/conn h-k.gb" />
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90 <element name="conn j-k" value="emma_parts/conn j-k.gb" />
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91 <element name="conn l-n" value="emma_parts/conn l-n.gb" />
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92 <element name="conn l-r" value="emma_parts/conn l-r.gb" />
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93 <element name="conn l-w" value="emma_parts/conn l-w.gb" />
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94 <element name="conn l-y" value="emma_parts/conn l-y.gb" />
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95 <element name="conn q-r" value="emma_parts/conn q-r.gb" />
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96 <element name="conn r-w" value="emma_parts/conn r-w.gb" />
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97 <element name="conn t-v" value="emma_parts/conn t-v.gb" />
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98 <element name="conn w-x" value="emma_parts/conn w-x.gb" />
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99 <element name="conn w-y" value="emma_parts/conn w-y.gb" />
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100 <element name="conn w-z" value="emma_parts/conn w-z.gb" />
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101 <element name="conn y-z" value="emma_parts/conn y-z.gb" />
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102 <element name="p10_tet-aptazyme" value="emma_parts/p10_tet-aptazyme.gb" />
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103 <element name="p11_sv40polya" value="emma_parts/p11_sv40polya.gb" />
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104 <element name="p14_cmvp" value="emma_parts/p14_cmvp.gb" />
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105 <element name="p14_sv40p" value="emma_parts/p14_sv40p.gb" />
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106 <element name="p15_puror" value="emma_parts/p15_puror.gb" />
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107 <element name="p16_bghpolya" value="emma_parts/p16_bghpolya.gb" />
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108 <element name="p18_cmvp" value="emma_parts/p18_cmvp.gb" />
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109 <element name="p18_ef1ap" value="emma_parts/p18_ef1ap.gb" />
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110 <element name="p19_mneogreen" value="emma_parts/p19_mneogreen.gb" />
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111 <element name="p19_mruby2" value="emma_parts/p19_mruby2.gb" />
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112 <element name="p19_mtagbfp2" value="emma_parts/p19_mtagbfp2.gb" />
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113 <element name="p19_tet-on-3g" value="emma_parts/p19_tet-on-3g.gb" />
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114 <element name="p1_5'-itr-pb" value="emma_parts/p1_5'-itr-pb.gb" />
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115 <element name="p1_5'ha-haavs1" value="emma_parts/p1_5'ha-haavs1.gb" />
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116 <element name="p20_ct-minute-nes" value="emma_parts/p20_ct-minute-nes.gb" />
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117 <element name="p20_ct-nes" value="emma_parts/p20_ct-nes.gb" />
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118 <element name="p20_linker3" value="emma_parts/p20_linker3.gb" />
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119 <element name="p20_p2a" value="emma_parts/p20_p2a.gb" />
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120 <element name="p21_dmra" value="emma_parts/p21_dmra.gb" />
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121 <element name="p21_mkate2" value="emma_parts/p21_mkate2.gb" />
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122 <element name="p21_mneogreen" value="emma_parts/p21_mneogreen.gb" />
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123 <element name="p21_mruby2" value="emma_parts/p21_mruby2.gb" />
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124 <element name="p21_mtagbfp2" value="emma_parts/p21_mtagbfp2.gb" />
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125 <element name="p21_puror" value="emma_parts/p21_puror.gb" />
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126 <element name="p22_pgkpolya" value="emma_parts/p22_pgkpolya.gb" />
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127 <element name="p23_insulatorfb" value="emma_parts/p23_insulatorfb.gb" />
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128 <element name="p24_3'ha_haavs1" value="emma_parts/p24_3'ha_haavs1.gb" />
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129 <element name="p24_3'pb" value="emma_parts/p24_3'pb.gb" />
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130 <element name="p25_sv40-ori" value="emma_parts/p25_sv40-ori.gb" />
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131 <element name="p2_insulatorfb" value="emma_parts/p2_insulatorfb.gb" />
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132 <element name="p3_cagp" value="emma_parts/p3_cagp.gb" />
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133 <element name="p3_cmvp_tet" value="emma_parts/p3_cmvp_tet.gb" />
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134 <element name="p3_ef1ap" value="emma_parts/p3_ef1ap.gb" />
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135 <element name="p3_tre3gp" value="emma_parts/p3_tre3gp.gb" />
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136 <element name="p4_kt-l7ae -weiss" value="emma_parts/p4_kt-l7ae -weiss.gb" />
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137 <element name="p4_lac-o" value="emma_parts/p4_lac-o.gb" />
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138 <element name="p5_attb-bxb1" value="emma_parts/p5_attb-bxb1.gb" />
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139 <element name="p5_attp-bxb1" value="emma_parts/p5_attp-bxb1.gb" />
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140 <element name="p5_k1-k1" value="emma_parts/p5_k1-k1.gb" />
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141 <element name="p5_kt-weiss" value="emma_parts/p5_kt-weiss.gb" />
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142 <element name="p6_atg_boxc" value="emma_parts/p6_atg_boxc.gb" />
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143 <element name="p6_kozak-atg" value="emma_parts/p6_kozak-atg.gb" />
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144 <element name="p6_nt-igkl sequence" value="emma_parts/p6_nt-igkl sequence.gb" />
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145 <element name="p6_nt-mls" value="emma_parts/p6_nt-mls.gb" />
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146 <element name="p6_nt-myristoylation signal" value="emma_parts/p6_nt-myristoylation signal.gb" />
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147 <element name="p6_nt-palm sequence" value="emma_parts/p6_nt-palm sequence.gb" />
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148 <element name="p6_nt-sv40_nls" value="emma_parts/p6_nt-sv40_nls.gb" />
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149 <element name="p7_bxb1" value="emma_parts/p7_bxb1.gb" />
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150 <element name="p7_l7ae-weiss" value="emma_parts/p7_l7ae-weiss.gb" />
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151 <element name="p7_l7ae" value="emma_parts/p7_l7ae.gb" />
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152 <element name="p7_laci" value="emma_parts/p7_laci.gb" />
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153 <element name="p7_mcherry" value="emma_parts/p7_mcherry.gb" />
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154 <element name="p7_mkate2" value="emma_parts/p7_mkate2.gb" />
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155 <element name="p7_mneogreen" value="emma_parts/p7_mneogreen.gb" />
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156 <element name="p7_mruby2" value="emma_parts/p7_mruby2.gb" />
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157 <element name="p7_mtagbfp2" value="emma_parts/p7_mtagbfp2.gb" />
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158 <element name="p8_linker1" value="emma_parts/p8_linker1.gb" />
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159 <element name="p8_linker2" value="emma_parts/p8_linker2.gb" />
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160 <element name="p8_p2a" value="emma_parts/p8_p2a.gb" />
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161 <element name="p8a_ct-kdel" value="emma_parts/p8a_ct-kdel.gb" />
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162 <element name="p8b_ires2" value="emma_parts/p8b_ires2.gb" />
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163 <element name="p9_a-tubulin" value="emma_parts/p9_a-tubulin.gb" />
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164 <element name="p9_bsdr" value="emma_parts/p9_bsdr.gb" />
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165 <element name="p9_dmrc" value="emma_parts/p9_dmrc.gb" />
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166 <element name="p9_firefly luciferase" value="emma_parts/p9_firefly luciferase.gb" />
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167 <element name="p9_mneogreen" value="emma_parts/p9_mneogreen.gb" />
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168 <element name="p9_mruby2" value="emma_parts/p9_mruby2.gb" />
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169 <element name="p9_mtagbfp2" value="emma_parts/p9_mtagbfp2.gb" />
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170 <element name="p9_neor" value="emma_parts/p9_neor.gb" />
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171 <element name="p9_puror" value="emma_parts/p9_puror.gb" />
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172 </collection>
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173 </param>
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174 <param name="picklist" value="example_picklist.xls" />
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175 <param name="source_plate" value="example_echo_plate.xlsx"/>
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176 <param name="quantity_unit" value="fmol" />
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177 <param name="part_quantity" value="1.3" />
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178 <param name="buffer_volume" value="0.3" />
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179 <param name="total_volume" value="1.0" />
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180 <param name="dispenser" value="labcyte_echo" />
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181 <output name="output_zip" ftype='zip'>
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182 <assert_contents>
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183 <has_archive_member path=".*" n="5"/>
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184 </assert_contents>
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185 </output>
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186 </test>
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187 </tests>
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188
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189 <help><![CDATA[
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190 create_assembly_picklists
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191 =========================
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192
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193 Provide a source plate map and an assembly plan, get a robotic picklist spreadsheet for Tecan EVO or Labcyte Echo.
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194 `Read more... <https://github.com/Edinburgh-Genome-Foundry/Plateo/blob/master/README.rst>`_
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195
1
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196 **Advance parameter**:
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197 ---------------------
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198 * **Backbone Name(s)**: It can be one backbone or more than one (one name by line)
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199 * **Backbone Molar Ratio**: between 0.0 and 1.0
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200 This section is to multiplie the backbone concentration with the part:backbone molar ratio. This tricks the calculator into making a picklist with the desired ratio. For example, a part:backbone = 2:1 will multiply the backbone concentration by 2, therefore half as much of it will be added to the well.
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201 **If Part quantity unit is ng**: Backbone Molar Ratio calculation is not performed in this case.
0
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202 ]]></help>
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203 <citations>
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204 <citation type="bibtex">
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205 @unpublished{create_assembly_picklists
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206 author = {Ramiz Khaled},
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207 title = {{create_assembly_picklists}},
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208 url = {https://github.com/Edinburgh-Genome-Foundry/CUBA/blob/master/backend/app/views/create_assembly_picklists/CreateAssemblyPicklistsView.py},
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209 }
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210 </citation>
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211 </citations>
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212 </tool>