Mercurial > repos > iuc > data_manager_primer_scheme_bedfiles
comparison data_manager/install_primer_scheme_bedfiles.xml @ 6:dd451e45681c draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 4880dcfcdddd9ed8415ccde01b2f8e2c28dab5c3"
author | iuc |
---|---|
date | Tue, 16 Nov 2021 08:22:08 +0000 |
parents | be70da9dc013 |
children |
comparison
equal
deleted
inserted
replaced
5:be70da9dc013 | 6:dd451e45681c |
---|---|
1 <tool id="data_manager_primer_scheme_bedfiles" name="BED-format primer scheme data manager" version="0.0.12" tool_type="manage_data" profile="19.05"> | 1 <tool id="data_manager_primer_scheme_bedfiles" name="BED-format primer scheme data manager" version="0.0.13" tool_type="manage_data" profile="20.09"> |
2 <requirements> | 2 <requirements> |
3 <requirement type="package" version="2.24.0">requests</requirement> | 3 <requirement type="package" version="2.26.0">requests</requirement> |
4 </requirements> | 4 </requirements> |
5 <!-- fetch all the primers in one go --> | 5 <!-- fetch all the primers in one go --> |
6 <command detect_errors="exit_code"><![CDATA[ | 6 <command detect_errors="exit_code"><![CDATA[ |
7 python '$__tool_directory__/install_primer_scheme_bedfiles.py' | 7 python '$__tool_directory__/install_primer_scheme_bedfiles.py' |
8 '${output_file}' | 8 '${output_file}' |
9 #if $input.input_type == "ARTIC" | 9 #if $input.input_type == "network" |
10 --artic_primers '${input.primers}' | 10 ## this code looks up the existing table and uses it to build a list of known primers which |
11 ## is then used to filter the $input.primers variable. some notes: | |
12 ## | |
13 ## $__app__.tool_data_tables is a dictionary where the keys are data table names and the values | |
14 ## are TabularToolDataTable objects (from lib/galaxy/tools/data/__init__.py) | |
15 ## | |
16 ## the get_fields() method on the TabularToolDataTable returns a list of lists, with one list | |
17 ## per line of the tool data table, so row[0] is the first field (i.e. the value column) | |
18 ## | |
19 ## $input.primers is a string ('val1,val2') when interpreted outside of #set but a list inside of #set | |
20 ## | |
21 ## known_primers is the $known_primers variable but because it is in a list comprehension the $ should | |
22 ## not be used | |
23 #set $data_table = $__app__.tool_data_tables.get("primer_scheme_bedfiles") | |
24 #if $data_table is not None: | |
25 #set $known_primers = [ row[0] for row in $data_table.get_fields() ] | |
26 #set $primer_list = ','.join([ primer_name for primer_name in $input.primers if primer_name not in known_primers ]) | |
27 #else | |
28 #set $primer_list = $input.primers | |
29 #end if | |
30 --artic_primers '$primer_list' | |
11 #else | 31 #else |
12 --primer_file '${input.primer_input}' | 32 --primer_file '${input.primer_input}' |
13 --primer_name '${input.primer_name}' | 33 --primer_name '${input.primer_name}' |
14 --primer_description '${input.primer_description}' | 34 --primer_description '${input.primer_description}' |
15 #end if | 35 #end if |
16 ]]></command> | 36 ]]></command> |
17 <inputs> | 37 <inputs> |
18 <conditional name="input"> | 38 <conditional name="input"> |
19 <param name="input_type" label="Choose the source for primer schemes" type="select"> | 39 <param name="input_type" label="Choose the source for primer schemes" type="select"> |
20 <option value="ARTIC" selected="true">ARTIC SARS-CoV-2 Github page</option> | 40 <option value="network" selected="true">ARTIC SARS-CoV-2, VarSkip and Midnight web pages</option> |
21 <option value="history">History</option> | 41 <option value="history">History</option> |
22 </param> | 42 </param> |
23 <when value="ARTIC"> | 43 <when value="network"> |
24 <param name="primers" type="select" multiple="true" label="SARS-CoV-2 Primers to fetch"> | 44 <param name="primers" type="select" multiple="true" label="SARS-CoV-2 Primers to fetch"> |
25 <option value="SARS-CoV-2-ARTICv1" selected="true">SARS-CoV-2 ARTIC v1</option> | 45 <option value="SARS-CoV-2-ARTICv1" selected="true">SARS-CoV-2 ARTIC v1</option> |
26 <option value="SARS-CoV-2-ARTICv2" selected="true">SARS-CoV-2 ARTIC v2</option> | 46 <option value="SARS-CoV-2-ARTICv2" selected="true">SARS-CoV-2 ARTIC v2</option> |
27 <option value="SARS-CoV-2-ARTICv3" selected="true">SARS-CoV-2 ARTIC v3</option> | 47 <option value="SARS-CoV-2-ARTICv3" selected="true">SARS-CoV-2 ARTIC v3</option> |
48 <option value="SARS-CoV-2-ARTICv4" selected="true">SARS-CoV-2 ARTIC v4</option> | |
49 <option value="VarSkip-V1a" selected="true">NEB VarSkip-V1a</option> | |
50 <option value="Midnight-v1" selected="true">RAPID/Midnight v1</option> | |
28 </param> | 51 </param> |
29 </when> | 52 </when> |
30 <when value="history"> | 53 <when value="history"> |
31 <param name="primer_input" label="Select history item" type="data" format="bed" /> | 54 <param name="primer_input" label="Select history item" type="data" format="bed" /> |
32 <param name="primer_name" label="Name for this primer scheme" type="text" | 55 <param name="primer_name" label="Name for this primer scheme" type="text" |
33 help="Non-word characters will be removed from primer scheme name and spaces replaced with underscore (_)" /> | 56 help="Characters that are not word characters or - will be removed from primer scheme name and spaces replaced with underscore (_)" /> |
34 <param name="primer_description" label="Description for primer scheme" type="text" /> | 57 <param name="primer_description" label="Description for primer scheme" type="text" /> |
35 </when> | 58 </when> |
36 </conditional> | 59 </conditional> |
37 </inputs> | 60 </inputs> |
38 <outputs> | 61 <outputs> |
39 <data name="output_file" format="data_manager_json"/> | 62 <data name="output_file" format="data_manager_json"/> |
40 </outputs> | 63 </outputs> |
41 <tests> | 64 <tests> |
42 <test> | 65 <test> |
43 <param name="input_type" value="ARTIC" /> | 66 <param name="input_type" value="network" /> |
44 <param name="primers" value="SARS-CoV-2-ARTICv1,SARS-CoV-2-ARTICv2,SARS-CoV-2-ARTICv3"/> | 67 <param name="primers" value="SARS-CoV-2-ARTICv1,SARS-CoV-2-ARTICv2,SARS-CoV-2-ARTICv3,SARS-CoV-2-ARTICv4,VarSkip-V1a,Midnight-v1"/> |
45 <output name="output_file"> | 68 <output name="output_file" value="data_manager_primer_scheme_bedfiles.json.template" compare="re_match" /> |
46 <assert_contents> | |
47 <has_text text="ARTIC"/> | |
48 </assert_contents> | |
49 </output> | |
50 </test> | 69 </test> |
51 <test> | 70 <test> |
52 <param name="input_type" value="history" /> | 71 <param name="input_type" value="history" /> |
53 <param name="primer_input" ftype="bed" value="sample1.bed" /> | 72 <param name="primer_input" ftype="bed" value="sample1.bed" /> |
54 <param name="primer_name" value="sample_primer" /> | 73 <param name="primer_name" value="sample_primer" /> |
57 <assert_contents> | 76 <assert_contents> |
58 <has_text text="sample_primer"/> | 77 <has_text text="sample_primer"/> |
59 </assert_contents> | 78 </assert_contents> |
60 </output> | 79 </output> |
61 </test> | 80 </test> |
81 <test> | |
82 <param name="input_type" value="history" /> | |
83 <param name="primer_input" ftype="bed" value="sample1.bed" /> | |
84 <param name="primer_name" value="sample^primer" /> | |
85 <param name="primer_description" value="sample primer scheme" /> | |
86 <output name="output_file"> | |
87 <assert_contents> | |
88 <has_text text="sampleprimer"/> | |
89 </assert_contents> | |
90 </output> | |
91 </test> | |
62 </tests> | 92 </tests> |
63 <help><![CDATA[ | 93 <help><![CDATA[ |
64 Amplicon sequencing for viral pathogens using the ARTIC_ pipeline or `PrimalSeq and iVar`_ relies on | 94 Amplicon sequencing for viral pathogens using the ARTIC_ pipeline or `PrimalSeq and iVar`_ relies on |
65 identifying primer locations in a reference sequence using BED format files. This | 95 identifying primer locations in a reference sequence using BED format files. This |
66 data manager populates a Galaxy tool data table, either from files provided via | 96 data manager populates a Galaxy tool data table, either from files provided via |
67 a history or via the ARTIC_ network Github repository. | 97 a history or via the ARTIC_, the New England Biolabs VarSkip_ and the Massey |
98 University Midnight_ web pages. | |
99 | |
100 If the data manager fails with an error message about downloading some of the primer data files, | |
101 try and visit the corresponding website to see if it is functioning correctly. As with anything | |
102 network-dependent, problems can sometimes happen. A simple solution is to wait some time and | |
103 run the data manager again. | |
104 | |
105 Finally, the data manager is designed to not duplicate primer files, so primers schemes that have | |
106 already been downloaded will be skipped when the install from network download mode is used. | |
68 | 107 |
69 .. _PrimalSeq and iVar: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1618-7 | 108 .. _PrimalSeq and iVar: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1618-7 |
70 .. _ARTIC: https://artic.network/ | 109 .. _ARTIC: https://artic.network/ |
110 .. _VarSkip: https://github.com/nebiolabs/VarSkip/ | |
111 .. _Midnight: https://zenodo.org/record/3897530#.XwM3ApMzZ0v | |
112 .. here_: https://gist.github.com/pvanheus/8403813b77e44cbd18e3fb1b3ca1b624 | |
71 ]]></help> | 113 ]]></help> |
72 <citations> | 114 <citations> |
73 <citation type="doi">10.1186/s13059-018-1618-7</citation> | 115 <citation type="doi">10.1186/s13059-018-1618-7</citation> |
74 </citations> | 116 </citations> |
75 </tool> | 117 </tool> |