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comparison domestication.xml @ 0:8fd9af4cb080 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, 12 May 2025 10:21:24 +0000
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1 <tool id="domestication" name="domestication" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
2 <description>Enables rapid and accurate preparation of DNA parts for modular cloning systems, such as Golden Gate Assembly</description>
3 <macros>
4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@TOOL_VERSION@">0.1.0</token>
6 </macros>
7 <requirements>
8 <requirement type="package" version="0.1.11">flametree</requirement>
9 <requirement type="package" version="1.85"> biopython </requirement>
10 <requirement type="package" version="0.1.10">proglog</requirement>
11 <requirement type="package" version="0.2.1">genedom</requirement>
12 <requirement type="package" version="2.2.3">pandas</requirement>
13 <requirement type="package" version="2.0.11">dnacauldron</requirement>
14 <requirement type="package" version="0.3.9">pdf-reports</requirement>
15 <requirement type="package" version="0.1.7">sequenticon</requirement>
16 <requirement type="package" version="3.1.4">dna_features_viewer</requirement>
17 </requirements>
18 <command detect_errors="exit_code"><![CDATA[
19 #set $file_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $genbank_files])
20 mkdir 'outdir_gb' && mkdir 'outdir_zip' &&
21 python '$__tool_directory__/domestication.py'
22 --files_to_domestication '$genbank_files'
23 --csv_file '$domestication_csv'
24 --file_name_mapping '$file_name_mapping'
25 --use_file_names_as_id '$adv.use_file_names_as_ids'
26 --allow_edits '$adv.allow_edits'
27 --output_dom 'output_zip.zip'
28 --output_methprot 'outdir_gb'
29 --methylation_protection '$methylation_protection' &&
30 cp 'output_zip.zip' '$output_zip'
31 ]]></command>
32 <inputs>
33 <param name="genbank_files" type="data" format="genbank" multiple="true" label="GenBank File(s)"/>
34 <param name="domestication_csv" type="data" format="csv" label="deomestication csv"/>
35 <param name="methylation_protection" type="boolean" checked="False" label="Enabel Methylation Protection"/>
36 <section name="adv" title="Advanced Options" expanded="false">
37 <param name="use_file_names_as_ids" type="boolean" checked="True" label="Use file names as sequence IDs?" />
38 <param name="allow_edits" type="boolean" checked="True" label="Allow sequence edits" help="If False, sequences cannot be edited by the domesticator, only extended
39 with flanks. If a sequence has for instance forbidden restriction sites,
40 the domesticaton will fail for this sequence (and this will be noted in
41 the report."/>
42 </section>
43 </inputs>
44 <outputs>
45 <data format="zip" name="output_zip" label="domestication results"/>
46 <collection name="methprot_gb" type="list" label="GenBank Files methylation protected">
47 <filter>methylation_protection == True</filter>
48 <discover_datasets pattern="(?P&lt;name&gt;.*).gb" format="genbank" directory="outdir_gb" />
49 </collection>
50 </outputs>
51 <tests>
52 <!--test without methylation protection-->
53 <test expect_num_outputs="1">
54 <param name="genbank_files" value="EMMA_undomesticated_parts/p3_2_CAG.gb,EMMA_undomesticated_parts/p7_gfp_sequence.gb,EMMA_undomesticated_parts/p14_CMVp.gb,EMMA_undomesticated_parts/p16_bGHpolyA.gb,EMMA_undomesticated_parts/p18_CMVp.gb,EMMA_undomesticated_parts/p19_mNeoGreen.gb,EMMA_undomesticated_parts/p22_PGKpolyA.gb" />
55 <param name="domestication_csv" value="EMMA.csv" />
56 <param name='methylation_protection' value='false' />
57 <param name="adv|use_file_names_as_ids" value="True" />
58 <param name="adv|allow_edits" value="True" />
59 <output name="output_zip" ftype='zip'>
60 <assert_contents>
61 <has_archive_member path=".*" n="24"/>
62 <has_archive_member path="order_ids.csv">
63 <has_n_lines n="8" />
64 </has_archive_member>
65 </assert_contents>
66 </output>
67 </test>
68 <!--test with methylation protection-->
69 <test expect_num_outputs="2">
70 <param name="genbank_files" value="EMMA_undomesticated_parts/p3_2_CAG.gb,EMMA_undomesticated_parts/p7_gfp_sequence.gb,EMMA_undomesticated_parts/p14_CMVp.gb,EMMA_undomesticated_parts/p16_bGHpolyA.gb,EMMA_undomesticated_parts/p18_CMVp.gb,EMMA_undomesticated_parts/p19_mNeoGreen.gb,EMMA_undomesticated_parts/p22_PGKpolyA.gb" />
71 <param name="domestication_csv" value="EMMA.csv" />
72 <param name="methylation_protection" value="true" />
73 <param name="adv|use_file_names_as_ids" value="True" />
74 <param name="adv|allow_edits" value="True" />
75 <output name="output_zip" ftype='zip'>
76 <assert_contents>
77 <has_archive_member path=".*" n="24"/>
78 <has_archive_member path="order_ids.csv">
79 <has_n_lines n="8" />
80 </has_archive_member>
81 </assert_contents>
82 </output>
83 <output_collection name="methprot_gb" type="list" count="7">
84 <element name="p14_CMVp">
85 <assert_contents>
86 <has_n_lines min="20" />
87 </assert_contents>
88 </element>
89 <element name="p16_bGHpolyA">
90 <assert_contents>
91 <has_n_lines min="20" />
92 </assert_contents>
93 </element>
94 <element name="p18_CMVp">
95 <assert_contents>
96 <has_n_lines min="20" />
97 </assert_contents>
98 </element>
99 <element name="p19_mNeoGreen">
100 <assert_contents>
101 <has_n_lines min="20" />
102 </assert_contents>
103 </element>
104 <element name="p22_PGKpolyA">
105 <assert_contents>
106 <has_n_lines min="20" />
107 </assert_contents>
108 </element>
109 <element name="p3_2_CAG">
110 <assert_contents>
111 <has_n_lines min="20" />
112 </assert_contents>
113 </element>
114 <element name="p7_gfp_sequence">
115 <assert_contents>
116 <has_n_lines min="20" />
117 </assert_contents>
118 </element>
119 </output_collection>
120 </test>
121 </tests>
122 <help><![CDATA[
123 Domestication
124 =================
125
126 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/>_`)
127 This tool streamlines the domestication process by identifying and removing internal restriction site like "BsaI_site", "NotI_site", "XbaI_site"... or costumised like "5x3mer" means "any 5 consecutive 3-nucleotide sequences — typically 5 unique 3-mers in a row.
128 ]]></help>
129 <citations>
130 <citation type="bibtex">
131 @unpublished{domestication
132 author = {Ramiz Khaled},
133 title = {{domestication}},
134 url = {https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb},
135 }
136 </citation>
137 </citations>
138 </tool>