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annotate domestication.xml @ 6:e0cda353d4cc draft

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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Mon, 19 May 2025 13:41:02 +0000
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children 70895bec2486
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8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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1 <tool id="domestication" name="domestication" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
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2 <description>Enables rapid and accurate preparation of DNA parts for modular cloning systems, such as Golden Gate Assembly</description>
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3 <macros>
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4 <token name="@VERSION_SUFFIX@">1</token>
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5 <token name="@TOOL_VERSION@">0.1.0</token>
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="0.1.11">flametree</requirement>
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9 <requirement type="package" version="1.85"> biopython </requirement>
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10 <requirement type="package" version="0.1.10">proglog</requirement>
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11 <requirement type="package" version="0.2.2">genedom</requirement>
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12 <requirement type="package" version="2.2.3">pandas</requirement>
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13 <requirement type="package" version="2.0.12">dnacauldron</requirement>
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14 <requirement type="package" version="0.3.9">pdf-reports</requirement>
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15 <requirement type="package" version="0.1.8">sequenticon</requirement>
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16 <requirement type="package" version="3.1.5">dna_features_viewer</requirement>
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17 </requirements>
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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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 $genbank_files])
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21 mkdir 'metoutdir_gb' && mkdir 'outdir_zip' && mkdir 'outdir_gb'&&
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8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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22 python '$__tool_directory__/domestication.py'
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bf8cd9487e33 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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23 --files_to_domestication '$genbank_file_paths'
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24 --csv_file '$domestication_csv'
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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25 --file_name_mapping '$file_name_mapping'
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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26 --use_file_names_as_id '$adv.use_file_names_as_ids'
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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27 --allow_edits '$adv.allow_edits'
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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28 --output_dom 'output_zip.zip'
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29 --output_gb_dom 'outdir_gb'
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30 --output_methprot 'metoutdir_gb'
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31 --methylation_protection '$methylation_protection' &&
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32 cp 'output_zip.zip' '$output_zip'
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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33 ]]></command>
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34 <inputs>
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35 <param name="genbank_files" type="data_collection" collection_type="list" format="genbank" label="GenBank File(s)"/>
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36 <param name="domestication_csv" type="data" format="csv" label="deomestication csv"/>
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37 <param name="methylation_protection" type="boolean" checked="False" label="Enabel Methylation Protection"/>
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8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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38 <section name="adv" title="Advanced Options" expanded="false">
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39 <param name="use_file_names_as_ids" type="boolean" checked="True" label="Use file names as sequence IDs?" />
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40 <param name="allow_edits" type="boolean" checked="True" label="Allow sequence edits" help="If False, sequences cannot be edited by the domesticator, only extended
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41 with flanks. If a sequence has for instance forbidden restriction sites,
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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42 the domesticaton will fail for this sequence (and this will be noted in
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43 the report."/>
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44 </section>
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45 </inputs>
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46 <outputs>
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47 <data format="zip" name="output_zip" label="domestication results"/>
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48 <collection name="domesticated_gb" type="list" label="Domesticated GenBank Files">
f78651af72e4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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49 <filter>methylation_protection == False</filter>
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50 <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir_gb" />
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51 </collection>
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52 <collection name="methprot_gb" type="list" label="GenBank Files methylation protected">
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53 <filter>methylation_protection == True</filter>
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54 <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="metoutdir_gb" />
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55 </collection>
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56 </outputs>
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57 <tests>
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58 <!--test without methylation protection-->
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59 <test expect_num_outputs="2">
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60 <param name="genbank_files">
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61 <collection type="list">
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62 <element name="p3_2_CAG" value="EMMA_undomesticated_parts/p3_2_CAG.gb" />
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63 <element name="p7_gfp_sequence" value="EMMA_undomesticated_parts/p7_gfp_sequence.gb" />
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64 <element name="p14_CMVp" value="EMMA_undomesticated_parts/p14_CMVp.gb" />
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65 <element name="p16_bGHpolyA" value="EMMA_undomesticated_parts/p16_bGHpolyA.gb" />
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66 <element name="p18_CMVp" value="EMMA_undomesticated_parts/p18_CMVp.gb" />
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67 <element name="p19_mNeoGreen" value="EMMA_undomesticated_parts/p19_mNeoGreen.gb" />
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68 <element name="p22_PGKpolyA" value="EMMA_undomesticated_parts/p22_PGKpolyA.gb" />
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69 </collection>
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70 </param>
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71 <param name="domestication_csv" value="EMMA.csv" />
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72 <param name='methylation_protection' value='false' />
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73 <param name="adv|use_file_names_as_ids" value="True" />
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74 <param name="adv|allow_edits" value="True" />
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75 <output name="output_zip" ftype='zip'>
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76 <assert_contents>
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77 <has_archive_member path=".*" n="24"/>
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78 <has_archive_member path="order_ids.csv">
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79 <has_n_lines n="8" />
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80 </has_archive_member>
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81 </assert_contents>
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82 </output>
4
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83 <output_collection name="domesticated_gb" type="list" count="7">
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84 <element name="p14_CMVp">
f78651af72e4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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85 <assert_contents>
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86 <has_n_lines min="20" />
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87 </assert_contents>
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88 </element>
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89 <element name="p16_bGHpolyA">
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90 <assert_contents>
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91 <has_n_lines min="20" />
f78651af72e4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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92 </assert_contents>
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93 </element>
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94 <element name="p18_CMVp">
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95 <assert_contents>
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96 <has_n_lines min="20" />
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97 </assert_contents>
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98 </element>
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99 <element name="p19_mNeoGreen">
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100 <assert_contents>
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101 <has_n_lines min="20" />
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102 </assert_contents>
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103 </element>
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104 <element name="p22_PGKpolyA">
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105 <assert_contents>
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106 <has_n_lines min="20" />
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107 </assert_contents>
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108 </element>
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109 <element name="p3_2_CAG">
f78651af72e4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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110 <assert_contents>
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111 <has_n_lines min="20" />
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112 </assert_contents>
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113 </element>
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114 <element name="p7_gfp_sequence">
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115 <assert_contents>
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116 <has_n_lines min="20" />
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117 </assert_contents>
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118 </element>
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119 </output_collection>
0
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120 </test>
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121 <!--test with methylation protection-->
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122 <test expect_num_outputs="2">
1
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123 <param name="genbank_files">
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124 <collection type="list">
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125 <element name="p3_2_CAG" value="EMMA_undomesticated_parts/p3_2_CAG.gb" />
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126 <element name="p7_gfp_sequence" value="EMMA_undomesticated_parts/p7_gfp_sequence.gb" />
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127 <element name="p14_CMVp" value="EMMA_undomesticated_parts/p14_CMVp.gb" />
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128 <element name="p16_bGHpolyA" value="EMMA_undomesticated_parts/p16_bGHpolyA.gb" />
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129 <element name="p18_CMVp" value="EMMA_undomesticated_parts/p18_CMVp.gb" />
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130 <element name="p19_mNeoGreen" value="EMMA_undomesticated_parts/p19_mNeoGreen.gb" />
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131 <element name="p22_PGKpolyA" value="EMMA_undomesticated_parts/p22_PGKpolyA.gb" />
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132 </collection>
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133 </param>
0
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134 <param name="domestication_csv" value="EMMA.csv" />
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135 <param name="methylation_protection" value="true" />
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136 <param name="adv|use_file_names_as_ids" value="True" />
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137 <param name="adv|allow_edits" value="True" />
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138 <output name="output_zip" ftype='zip'>
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139 <assert_contents>
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140 <has_archive_member path=".*" n="24"/>
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141 <has_archive_member path="order_ids.csv">
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142 <has_n_lines n="8" />
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143 </has_archive_member>
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144 </assert_contents>
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145 </output>
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146 <output_collection name="methprot_gb" type="list" count="7">
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147 <element name="p14_CMVp">
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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148 <assert_contents>
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149 <has_n_lines min="20" />
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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150 </assert_contents>
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151 </element>
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152 <element name="p16_bGHpolyA">
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153 <assert_contents>
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154 <has_n_lines min="20" />
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155 </assert_contents>
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156 </element>
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157 <element name="p18_CMVp">
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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158 <assert_contents>
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159 <has_n_lines min="20" />
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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160 </assert_contents>
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161 </element>
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162 <element name="p19_mNeoGreen">
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163 <assert_contents>
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164 <has_n_lines min="20" />
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165 </assert_contents>
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166 </element>
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167 <element name="p22_PGKpolyA">
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168 <assert_contents>
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169 <has_n_lines min="20" />
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170 </assert_contents>
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171 </element>
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172 <element name="p3_2_CAG">
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173 <assert_contents>
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174 <has_n_lines min="20" />
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175 </assert_contents>
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176 </element>
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177 <element name="p7_gfp_sequence">
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178 <assert_contents>
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179 <has_n_lines min="20" />
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180 </assert_contents>
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181 </element>
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182 </output_collection>
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183 </test>
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184 </tests>
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185 <help><![CDATA[
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186 Domestication
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187 =================
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188
4
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189 The Domestication Tool in the EGF Biofoundry, powered by Genedom, enables rapid and accurate preparation of DNA parts for modular cloning systems, such as Golden Gate Assembly (complete documentation `here <https://edinburgh-genome-foundry.github.io/genedom/>`_)
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190 This tool streamlines the domestication process by identifying and removing internal restriction site like "BsaI_site", "NotI_site", "XbaI_site"...(`enzyme dict <https://github.com/biopython/biopython/blob/master/Bio/Restriction/Restriction_Dictionary.py>`_ ) or costumised like "5x3mer" means "any 5 consecutive 3-nucleotide sequences — typically 5 unique 3-mers in a row.
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191
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192 **Parameters**:
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193 ---------------
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194 * **GenBank File(s)**: GenBank files for domestication (can be output of sculpt tool)
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195 * **deomestication csv**: csv file containes the construct names with their parts.`example <https://cuba.genomefoundry.org/static/file_examples/domesticate_part_batches/EMMA.csv>`_
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196 * **Enabel Methylation Protection**: Enable the methylation protection.
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197 * **Allow sequence edits**: Recommanded. If False, sequences cannot be edited by the domesticator, only extended with flanks. If a sequence has for instance forbidden restriction sites, the domesticaton will fail for this sequence (and this will be noted in the report.
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198 * **Use file names as sequence IDs?**: Recommended if the GenBank file names represent the fragment names.
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199 * **output**: Zip report for domestication process + domesticated gb files (methylation pretected in case of enable of methylation protecton option).
0
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200 ]]></help>
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201 <citations>
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202 <citation type="bibtex">
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203 @unpublished{domestication
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204 author = {Ramiz Khaled},
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205 title = {{domestication}},
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206 url = {https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb},
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207 }
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208 </citation>
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209 </citations>
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210 </tool>