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annotate domestication.xml @ 8:4bfdec0be6b1 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 Fri, 23 May 2025 09:04:43 +0000
parents 70895bec2486
children 450ed9dca5d5
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4bfdec0be6b1 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 Of New Parts" 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>
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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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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f730b81671fb planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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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 $genbank_files])
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f78651af72e4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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21 mkdir 'metoutdir_gb' && mkdir 'outdir_zip' && mkdir 'outdir_gb'&&
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22 cp '$domestication_csv' 'domestication_csv.csv' &&
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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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23 python '$__tool_directory__/domestication.py'
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bf8cd9487e33 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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24 --files_to_domestication '$genbank_file_paths'
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25 --csv_file 'domestication_csv.csv'
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26 --file_name_mapping '$file_name_mapping'
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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27 --use_file_names_as_id '$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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28 --allow_edits '$adv.allow_edits'
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29 --output_dom 'output_zip.zip'
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30 --output_gb_dom 'outdir_gb'
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31 --output_methprot 'metoutdir_gb'
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32 --methylation_protection '$methylation_protection' &&
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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33 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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34 ]]></command>
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35 <inputs>
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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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36 <param name="genbank_files" type="data_collection" collection_type="list" format="genbank" label="GenBank File(s)"/>
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37 <param name="domestication_csv" type="data" format="csv" label="Deomestication csv"/>
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e0cda353d4cc planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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38 <param name="methylation_protection" type="boolean" checked="False" label="Enabel Methylation Protection"/>
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39 <section name="adv" title="Advanced Options" expanded="false">
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40 <param name="use_file_names_as_ids" type="boolean" checked="True" label="Use File Names As Sequence IDs" />
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41 <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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42 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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43 the domesticaton will fail for this sequence (and this will be noted in
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44 the report."/>
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45 </section>
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46 </inputs>
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47 <outputs>
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48 <data format="zip" name="output_zip" label="domestication results"/>
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49 <collection name="domesticated_gb" type="list" label="Domesticated GenBank Files">
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50 <filter>methylation_protection == False</filter>
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51 <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir_gb" />
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52 </collection>
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53 <collection name="methprot_gb" type="list" label="GenBank Files methylation protected">
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54 <filter>methylation_protection == True</filter>
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55 <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="metoutdir_gb" />
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56 </collection>
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57 </outputs>
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58 <tests>
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59 <!--test without methylation protection-->
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60 <test expect_num_outputs="2">
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61 <param name="genbank_files">
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62 <collection type="list">
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63 <element name="p3_2_CAG" value="EMMA_undomesticated_parts/p3_2_CAG.gb" />
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64 <element name="p7_gfp_sequence" value="EMMA_undomesticated_parts/p7_gfp_sequence.gb" />
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65 <element name="p14_CMVp" value="EMMA_undomesticated_parts/p14_CMVp.gb" />
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66 <element name="p16_bGHpolyA" value="EMMA_undomesticated_parts/p16_bGHpolyA.gb" />
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67 <element name="p18_CMVp" value="EMMA_undomesticated_parts/p18_CMVp.gb" />
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68 <element name="p19_mNeoGreen" value="EMMA_undomesticated_parts/p19_mNeoGreen.gb" />
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69 <element name="p22_PGKpolyA" value="EMMA_undomesticated_parts/p22_PGKpolyA.gb" />
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70 </collection>
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71 </param>
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72 <param name="domestication_csv" value="EMMA.csv" />
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73 <param name='methylation_protection' value='false' />
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74 <param name="adv|use_file_names_as_ids" value="True" />
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75 <param name="adv|allow_edits" value="True" />
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76 <output name="output_zip" ftype='zip'>
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77 <assert_contents>
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78 <has_archive_member path=".*" n="24"/>
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79 <has_archive_member path="order_ids.csv">
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80 <has_n_lines n="8" />
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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81 </has_archive_member>
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82 </assert_contents>
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83 </output>
4
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84 <output_collection name="domesticated_gb" type="list" count="7">
f78651af72e4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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85 <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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86 <assert_contents>
f78651af72e4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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87 <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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88 </assert_contents>
f78651af72e4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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89 </element>
f78651af72e4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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90 <element name="p16_bGHpolyA">
f78651af72e4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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91 <assert_contents>
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92 <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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93 </assert_contents>
f78651af72e4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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94 </element>
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95 <element name="p18_CMVp">
f78651af72e4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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96 <assert_contents>
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97 <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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98 </assert_contents>
f78651af72e4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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99 </element>
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100 <element name="p19_mNeoGreen">
f78651af72e4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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101 <assert_contents>
f78651af72e4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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102 <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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103 </assert_contents>
f78651af72e4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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104 </element>
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105 <element name="p22_PGKpolyA">
f78651af72e4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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106 <assert_contents>
f78651af72e4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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107 <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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108 </assert_contents>
f78651af72e4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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109 </element>
f78651af72e4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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110 <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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111 <assert_contents>
f78651af72e4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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112 <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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113 </assert_contents>
f78651af72e4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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114 </element>
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115 <element name="p7_gfp_sequence">
f78651af72e4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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116 <assert_contents>
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117 <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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118 </assert_contents>
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119 </element>
f78651af72e4 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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120 </output_collection>
0
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121 </test>
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122 <!--test with methylation protection-->
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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123 <test expect_num_outputs="2">
1
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124 <param name="genbank_files">
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125 <collection type="list">
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126 <element name="p3_2_CAG" value="EMMA_undomesticated_parts/p3_2_CAG.gb" />
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127 <element name="p7_gfp_sequence" value="EMMA_undomesticated_parts/p7_gfp_sequence.gb" />
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128 <element name="p14_CMVp" value="EMMA_undomesticated_parts/p14_CMVp.gb" />
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129 <element name="p16_bGHpolyA" value="EMMA_undomesticated_parts/p16_bGHpolyA.gb" />
bf8cd9487e33 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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130 <element name="p18_CMVp" value="EMMA_undomesticated_parts/p18_CMVp.gb" />
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131 <element name="p19_mNeoGreen" value="EMMA_undomesticated_parts/p19_mNeoGreen.gb" />
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132 <element name="p22_PGKpolyA" value="EMMA_undomesticated_parts/p22_PGKpolyA.gb" />
bf8cd9487e33 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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133 </collection>
bf8cd9487e33 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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134 </param>
0
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135 <param name="domestication_csv" value="EMMA.csv" />
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136 <param name="methylation_protection" value="true" />
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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137 <param name="adv|use_file_names_as_ids" value="True" />
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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138 <param name="adv|allow_edits" value="True" />
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139 <output name="output_zip" ftype='zip'>
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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140 <assert_contents>
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141 <has_archive_member path=".*" n="24"/>
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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142 <has_archive_member path="order_ids.csv">
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143 <has_n_lines n="8" />
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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144 </has_archive_member>
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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145 </assert_contents>
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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146 </output>
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147 <output_collection name="methprot_gb" type="list" count="7">
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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148 <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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149 <assert_contents>
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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150 <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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151 </assert_contents>
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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152 </element>
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153 <element name="p16_bGHpolyA">
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154 <assert_contents>
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155 <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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156 </assert_contents>
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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157 </element>
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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158 <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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159 <assert_contents>
8fd9af4cb080 planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
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160 <has_n_lines min="20" />
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161 </assert_contents>
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162 </element>
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163 <element name="p19_mNeoGreen">
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164 <assert_contents>
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165 <has_n_lines min="20" />
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166 </assert_contents>
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167 </element>
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168 <element name="p22_PGKpolyA">
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169 <assert_contents>
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170 <has_n_lines min="20" />
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171 </assert_contents>
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172 </element>
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173 <element name="p3_2_CAG">
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174 <assert_contents>
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175 <has_n_lines min="20" />
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176 </assert_contents>
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177 </element>
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178 <element name="p7_gfp_sequence">
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179 <assert_contents>
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180 <has_n_lines min="20" />
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181 </assert_contents>
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182 </element>
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183 </output_collection>
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184 </test>
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185 </tests>
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186 <help><![CDATA[
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187 Domestication Of New Parts
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188 ==========================
0
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189
8
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190 The Domestication tool from the EGF Biofoundry, powered by Genedom, enables rapid and accurate add of the flanking enzyme sites to each DNA part preparing it for modular cloning systems, such as Golden Gate Assembly (complete documentation `here <https://edinburgh-genome-foundry.github.io/genedom/>`_)
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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).
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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>