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comparison domestication.xml @ 1:bf8cd9487e33 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 Tue, 13 May 2025 07:22:36 +0000
parents 8fd9af4cb080
children f730b81671fb
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0:8fd9af4cb080 1:bf8cd9487e33
1 <tool id="domestication" name="domestication" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> 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> 2 <description>Enables rapid and accurate preparation of DNA parts for modular cloning systems, such as Golden Gate Assembly</description>
3 <macros> 3 <macros>
4 <token name="@VERSION_SUFFIX@">0</token> 4 <token name="@VERSION_SUFFIX@">1</token>
5 <token name="@TOOL_VERSION@">0.1.0</token> 5 <token name="@TOOL_VERSION@">0.1.0</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="0.1.11">flametree</requirement> 8 <requirement type="package" version="0.1.11">flametree</requirement>
9 <requirement type="package" version="1.85"> biopython </requirement> 9 <requirement type="package" version="1.85"> biopython </requirement>
10 <requirement type="package" version="0.1.10">proglog</requirement> 10 <requirement type="package" version="0.1.10">proglog</requirement>
11 <requirement type="package" version="0.2.1">genedom</requirement> 11 <requirement type="package" version="0.2.1">genedom</requirement>
12 <requirement type="package" version="2.2.3">pandas</requirement> 12 <requirement type="package" version="2.2.3">pandas</requirement>
13 <requirement type="package" version="2.0.11">dnacauldron</requirement> 13 <requirement type="package" version="2.0.11">dnacauldron</requirement>
14 <requirement type="package" version="0.3.9">pdf-reports</requirement> 14 <requirement type="package" version="0.3.9">pdf-reports</requirement>
15 <requirement type="package" version="0.1.7">sequenticon</requirement> 15 <requirement type="package" version="0.1.8">sequenticon</requirement>
16 <requirement type="package" version="3.1.4">dna_features_viewer</requirement> 16 <requirement type="package" version="3.1.4">dna_features_viewer</requirement>
17 </requirements> 17 </requirements>
18 <command detect_errors="exit_code"><![CDATA[ 18 <command detect_errors="exit_code"><![CDATA[
19 #set genbank_file_paths = ','.join([str(f) for f in $genbank_files])
19 #set $file_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $genbank_files]) 20 #set $file_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $genbank_files])
20 mkdir 'outdir_gb' && mkdir 'outdir_zip' && 21 mkdir 'outdir_gb' && mkdir 'outdir_zip' &&
21 python '$__tool_directory__/domestication.py' 22 python '$__tool_directory__/domestication.py'
22 --files_to_domestication '$genbank_files' 23 --files_to_domestication '$genbank_file_paths'
23 --csv_file '$domestication_csv' 24 --csv_file '$domestication_csv'
24 --file_name_mapping '$file_name_mapping' 25 --file_name_mapping '$file_name_mapping'
25 --use_file_names_as_id '$adv.use_file_names_as_ids' 26 --use_file_names_as_id '$adv.use_file_names_as_ids'
26 --allow_edits '$adv.allow_edits' 27 --allow_edits '$adv.allow_edits'
27 --output_dom 'output_zip.zip' 28 --output_dom 'output_zip.zip'
28 --output_methprot 'outdir_gb' 29 --output_methprot 'outdir_gb'
29 --methylation_protection '$methylation_protection' && 30 --methylation_protection '$methylation_protection' &&
30 cp 'output_zip.zip' '$output_zip' 31 cp 'output_zip.zip' '$output_zip'
31 ]]></command> 32 ]]></command>
32 <inputs> 33 <inputs>
33 <param name="genbank_files" type="data" format="genbank" multiple="true" label="GenBank File(s)"/> 34 <param name="genbank_files" type="data_collection" collection_type="list" format="genbank" label="GenBank File(s)"/>
34 <param name="domestication_csv" type="data" format="csv" label="deomestication csv"/> 35 <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 <param name="methylation_protection" type="boolean" checked="False" label="Enabel Methylation Protection"/>
36 <section name="adv" title="Advanced Options" expanded="false"> 37 <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="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 <param name="allow_edits" type="boolean" checked="True" label="Allow sequence edits" help="If False, sequences cannot be edited by the domesticator, only extended
49 </collection> 50 </collection>
50 </outputs> 51 </outputs>
51 <tests> 52 <tests>
52 <!--test without methylation protection--> 53 <!--test without methylation protection-->
53 <test expect_num_outputs="1"> 54 <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="genbank_files">
56 <collection type="list">
57 <element name="p3_2_CAG" value="EMMA_undomesticated_parts/p3_2_CAG.gb" />
58 <element name="p7_gfp_sequence" value="EMMA_undomesticated_parts/p7_gfp_sequence.gb" />
59 <element name="p14_CMVp" value="EMMA_undomesticated_parts/p14_CMVp.gb" />
60 <element name="p16_bGHpolyA" value="EMMA_undomesticated_parts/p16_bGHpolyA.gb" />
61 <element name="p18_CMVp" value="EMMA_undomesticated_parts/p18_CMVp.gb" />
62 <element name="p19_mNeoGreen" value="EMMA_undomesticated_parts/p19_mNeoGreen.gb" />
63 <element name="p22_PGKpolyA" value="EMMA_undomesticated_parts/p22_PGKpolyA.gb" />
64 </collection>
65 </param>
55 <param name="domestication_csv" value="EMMA.csv" /> 66 <param name="domestication_csv" value="EMMA.csv" />
56 <param name='methylation_protection' value='false' /> 67 <param name='methylation_protection' value='false' />
57 <param name="adv|use_file_names_as_ids" value="True" /> 68 <param name="adv|use_file_names_as_ids" value="True" />
58 <param name="adv|allow_edits" value="True" /> 69 <param name="adv|allow_edits" value="True" />
59 <output name="output_zip" ftype='zip'> 70 <output name="output_zip" ftype='zip'>
65 </assert_contents> 76 </assert_contents>
66 </output> 77 </output>
67 </test> 78 </test>
68 <!--test with methylation protection--> 79 <!--test with methylation protection-->
69 <test expect_num_outputs="2"> 80 <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" /> 81 <param name="genbank_files">
82 <collection type="list">
83 <element name="p3_2_CAG" value="EMMA_undomesticated_parts/p3_2_CAG.gb" />
84 <element name="p7_gfp_sequence" value="EMMA_undomesticated_parts/p7_gfp_sequence.gb" />
85 <element name="p14_CMVp" value="EMMA_undomesticated_parts/p14_CMVp.gb" />
86 <element name="p16_bGHpolyA" value="EMMA_undomesticated_parts/p16_bGHpolyA.gb" />
87 <element name="p18_CMVp" value="EMMA_undomesticated_parts/p18_CMVp.gb" />
88 <element name="p19_mNeoGreen" value="EMMA_undomesticated_parts/p19_mNeoGreen.gb" />
89 <element name="p22_PGKpolyA" value="EMMA_undomesticated_parts/p22_PGKpolyA.gb" />
90 </collection>
91 </param>
71 <param name="domestication_csv" value="EMMA.csv" /> 92 <param name="domestication_csv" value="EMMA.csv" />
72 <param name="methylation_protection" value="true" /> 93 <param name="methylation_protection" value="true" />
73 <param name="adv|use_file_names_as_ids" value="True" /> 94 <param name="adv|use_file_names_as_ids" value="True" />
74 <param name="adv|allow_edits" value="True" /> 95 <param name="adv|allow_edits" value="True" />
75 <output name="output_zip" ftype='zip'> 96 <output name="output_zip" ftype='zip'>