Mercurial > repos > tduigou > save_to_db

annotate seq_to_db.xml @ 0:7ff266aecf01 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
author tduigou
date Wed, 11 Jun 2025 09:42:24 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
1 <tool id="seq_to_db" name="Save Sequence Data In DB" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
2 <description>Save fragment's sequence in an accessible database and import it from .gb files</description>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
3 <macros>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
4 <token name="@VERSION_SUFFIX@">0</token>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
5 <token name="@TOOL_VERSION@">0.1.0</token>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
6 </macros>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
7 <requirements>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
8 <requirement type="package" version="2.2.3">pandas</requirement>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
9 <requirement type="package" version="2.0.40">sqlalchemy</requirement>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
10 <requirement type="package" version="2.9.9">psycopg2</requirement>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
11 </requirements>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
12 <command detect_errors="exit_code"><![CDATA[
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
13 #set genbank_file_paths = ','.join([str(f) for f in $genbank_files])
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
14 #set $file_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $genbank_files])
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
15 python '$__tool_directory__/save_to_db.py'
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
16 --input '$genbank_file_paths'
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
17 --sequence_column '$sequence_column'
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
18 --annotation_column '$annotation_column'
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
19 --db_uri '$db_uri'
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
20 --table '$table'
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
21 --fragment_column '$fragment_column'
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
22 --output '$output'
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
23 --file_name_mapping '$file_name_mapping'
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
24 --json_conf '$json_conf'
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
25 ]]></command>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
26 <inputs>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
27 <param name="genbank_files" type="data_collection" collection_type="list" format="genbank" label="GenBank File(s)"/>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
28 <param name="table" type="text" label="DB Table Name" optional="true" help="It can be extracted from JSON file -key:'JSON_table'-" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
29 <param name="sequence_column" type="text" label="DB Column Contains Sequence For ganbank File" optional="true" help="It can be extracted from JSON file -key:'JSON_sequence_column'-" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
30 <param name="annotation_column" type="text" label="DB Column Contains Annotation For Ganbank File" optional="true" help="It can be extracted from JSON file -key:'JSON_annotation_column'-" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
31 <param name="fragment_column" type="text" label="DB IDs Column Name" optional="true" help="It can be extracted from JSON file -key:'JSON_fragment_column'-" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
32 <param name="db_uri" type="text" label="DB Connection URI" help="postgresql://container_name:password@host:port/path/to/database (It can be extracted from JSON file -key:'JSON_db_uri'-)" optional="true" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
33 <section name='adv' title='Advance' expanded='false'>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
34 <param name="json_conf" type="data" format='json' label="DB config as a json file" help="JSON file specifying the database URI, table name and the column names for annotation and sequence data" optional="true" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
35 </section>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
36 </inputs>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
37 <outputs>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
38 <data name="output" format="txt" label="saving report" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
39 </outputs>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
40 <tests>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
41 <!--Only 1 test can be execute because the fragment will be already saved for the second test and it will return error as the fragments are present in the DB (execut ../get_db_data/testMock.py to regenerate initial DB)-->
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
42 <!--test tool blocking from JSON. It is commented because it should faild as it is a test to validate that the tool can be blocked from json file -->
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
43 <test>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
44 <param name="genbank_files">
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
45 <collection type="list">
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
46 <element name="p7_L7Ae-Weiss" value="p7_L7Ae-Weiss.gb" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
47 <element name="p7_gfp_sequence" value="p6_Nt-IgKLsequence.gb" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
48 <element name="p14_CMVp" value="p6_Kozak-ATG.gb" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
49 <element name="p16_bGHpolyA" value="p4_Kt-L7Ae-Weiss.gb" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
50 <element name="p18_CMVp" value="HC_Amp_ccdB.gb" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
51 </collection>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
52 </param>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
53 <param name="adv|json_conf" value="test-JSON_arg_block.json" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
54 <output name="output" file="test_raport.txt" ftype="txt" >
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
55 <assert_contents>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
56 <has_n_lines n="5" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
57 <has_line_matching expression="p7_L7Ae-Weiss" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
58 <has_line_matching expression="p6_Nt-IgKLsequence" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
59 <has_line_matching expression="p6_Kozak-ATG" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
60 <has_line_matching expression="p4_Kt-L7Ae-Weiss" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
61 <has_line_matching expression="HC_Amp_ccdB" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
62 </assert_contents>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
63 </output>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
64 </test>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
65 <!--test DB config in the tool -->
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
66 <test>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
67 <param name="genbank_files">
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
68 <collection type="list">
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
69 <element name="p7_L7Ae-Weiss" value="p7_L7Ae-Weiss.gb" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
70 <element name="p7_gfp_sequence" value="p6_Nt-IgKLsequence.gb" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
71 <element name="p14_CMVp" value="p6_Kozak-ATG.gb" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
72 <element name="p16_bGHpolyA" value="p4_Kt-L7Ae-Weiss.gb" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
73 <element name="p18_CMVp" value="HC_Amp_ccdB.gb" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
74 </collection>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
75 </param>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
76 <param name="table" value="sample" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
77 <param name="sequence_column" value="sequence" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
78 <param name="annotation_column" value="annotation" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
79 <param name="fragment_column" value="fragment" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
80 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
81 <output name="output" file="test_raport.txt" ftype="txt" >
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
82 <assert_contents>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
83 <has_n_lines n="5" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
84 <has_line_matching expression="p7_L7Ae-Weiss" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
85 <has_line_matching expression="p6_Nt-IgKLsequence" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
86 <has_line_matching expression="p6_Kozak-ATG" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
87 <has_line_matching expression="p4_Kt-L7Ae-Weiss" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
88 <has_line_matching expression="HC_Amp_ccdB" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
89 </assert_contents>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
90 </output>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
91 </test>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
92 <!--test DB config from JSON. It is commented because the save can be done only on time then the fragment willl be in the DB and it will return a failure. to run the test comment the test above (one saving test in the run)-->
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
93 <test>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
94 <param name="genbank_files">
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
95 <collection type="list">
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
96 <element name="p7_L7Ae-Weiss" value="p7_L7Ae-Weiss.gb" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
97 <element name="p7_gfp_sequence" value="p6_Nt-IgKLsequence.gb" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
98 <element name="p14_CMVp" value="p6_Kozak-ATG.gb" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
99 <element name="p16_bGHpolyA" value="p4_Kt-L7Ae-Weiss.gb" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
100 <element name="p18_CMVp" value="HC_Amp_ccdB.gb" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
101 </collection>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
102 </param>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
103 <param name="adv|json_conf" value="test-JSON_arg.json" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
104 <output name="output" file="test_raport.txt" ftype="txt" >
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
105 <assert_contents>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
106 <has_n_lines n="5" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
107 <has_line_matching expression="p7_L7Ae-Weiss" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
108 <has_line_matching expression="p6_Nt-IgKLsequence" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
109 <has_line_matching expression="p6_Kozak-ATG" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
110 <has_line_matching expression="p4_Kt-L7Ae-Weiss" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
111 <has_line_matching expression="HC_Amp_ccdB" />
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
112 </assert_contents>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
113 </output>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
114 </test>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
115 </tests>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
116
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
117 <help><![CDATA[
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
118 Save Sequence Data In DB
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
119 ========================
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
120
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
121 Implemented a system to save GenBank (.gb) files in an accessible DB, based on a connection via URI requests.
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
122
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
123 **Parameters**:
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
124 ---------------
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
125 * **GenBank File(s)**: List of GenBaks files.
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
126 * **DB Table Name**: Name of the target table in the PostgreSQL database.
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
127 * **DB Column Contains Sequence For ganbank File**: Column storing sequence data, expected to start with "ORIGIN".
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
128 * **DB Column Contains Annotation For Ganbank File**: Column containing annotation data, to save al part before "ORIGIN" in the .gb file.
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
129 * **DB IDs Column Name**: Column holding the unique fragment IDs.
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
130 * **DB Connection URI**: URI used to connect to the database (e.g., postgresql://postgres:pass@localhost:5432/test_fragments_db).
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
131 * **DB config as a json file**: JSON file contains the DB configuration:
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
132 - "JSON_table": will be the key to the table name.
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
133 - "JSON_sequence_column": will be the key to the sequence column.
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
134 - "JSON_annotation_column": will be the key to the annotation column.
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
135 - "JSON_fragment_column": will be the key to the fragment column.
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
136 - "JSON_db_uri": will be the key to the URI.
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
137 - "execution": It is the key to execute or block the tool during a workflow ("True" or "False").
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
138 ]]></help>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
139 <citations>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
140 <citation type="bibtex">
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
141 @unpublished{seq_to_db
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
142 author = {Ramiz Khaled},
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
143 title = {{seq_to_db}},
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
144 url = {https://github.com/brsynth/},
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
145 }
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
146 </citation>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
147 </citations>
7ff266aecf01 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
148 </tool>