Mercurial > repos > tduigou > seq_to_db

annotate seq_to_db.xml @ 2:dad2c4c3450a 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 db4ac861e1d03fcdfe94321d858839124e493930-dirty
author tduigou
date Wed, 23 Jul 2025 09:44:33 +0000
parents 3daf04425ea1
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9f845ccb1a9f 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">
9f845ccb1a9f 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>
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
3 <macros>
2
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
4 <token name="@VERSION_SUFFIX@">2</token>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
5 <token name="@TOOL_VERSION@">0.3.0</token>
0
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
6 </macros>
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
7 <requirements>
9f845ccb1a9f 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>
9f845ccb1a9f 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>
9f845ccb1a9f 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>
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
11 </requirements>
9f845ccb1a9f 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[
9f845ccb1a9f 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])
2
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
14 #set file_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $genbank_files])
0
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
15 python '$__tool_directory__/save_to_db.py'
2
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
16 --input '$genbank_file_paths'
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
17 --use_json_paramers '$json_use.use_json_paramers'
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
18 #if not $json_use.use_json_paramers:
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
19 --sequence_column '$json_use.sequence_column'
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
20 --annotation_column '$json_use.annotation_column'
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
21 --db_uri '$json_use.db_uri'
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
22 --table '$json_use.table'
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
23 --fragment_column '$json_use.fragment_column'
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
24 --execution_enable '$json_use.execution_enable'
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
25 #else:
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
26 --json_conf '$json_use.json_conf'
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
27 #end if
0
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
28 --output '$output'
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
29 --file_name_mapping '$file_name_mapping'
2
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
30 --json_generating '$json_generating'
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
31 --json_output '$json_output'
0
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
32 ]]></command>
2
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
33 <inputs>
0
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
34 <param name="genbank_files" type="data_collection" collection_type="list" format="genbank" label="GenBank File(s)"/>
2
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
35 <conditional name="json_use">
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
36 <param name="use_json_paramers" type="boolean" checked='false' label="Use parameters from JSON" help="extract parameters from json file" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
37 <when value="false">
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
38 <param name="execution_enable" type="boolean" checked='true' label="Send Requenst to DB" help="enable or desable the interaction with the DB (can be usefull in workflows)" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
39 <param name="table" type="text" label="DB Table Name" optional="true" help="It can be extracted from JSON file -key:'table'-" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
40 <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:'sequence_column'-" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
41 <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:'annotation_column'-" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
42 <param name="fragment_column" type="text" label="DB IDs Column Name" optional="true" help="It can be extracted from JSON file -key:'fragment_column'-" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
43 <param name="db_uri" type="text" label="DB Connection URI" help="postgresql://user_name:password@host:port/path/to/database (It can be extracted from JSON file -key:'db_uri'-)" optional="true" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
44 </when>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
45 <when value="true">
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
46 <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="false" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
47 </when>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
48 </conditional>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
49 <param name="json_generating" type="boolean" checked='true' label="Generat Parameters in JSON" help="generat parameters in json file" />
0
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
50 </inputs>
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
51 <outputs>
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
52 <data name="output" format="txt" label="saving report" />
2
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
53 <data name="json_output" format="json" label="seq_to_db_param">
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
54 <filter>json_generating == True</filter>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
55 </data>
0
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
56 </outputs>
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
57 <tests>
1
3daf04425ea1 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents: 0
diff changeset
58 <!--test tool blocking from galaxy. It is commented because it should faild as it is a test to validate that the tool can be blocked from json file -->
2
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
59 <test expect_num_outputs="2">
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
60 <param name="genbank_files">
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
61 <conditional type="list">
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
62 <element name="p7_L7Ae-Weiss" value="p7_L7Ae-Weiss.gb" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
63 <element name="p7_gfp_sequence" value="p6_Nt-IgKLsequence.gb" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
64 <element name="p14_CMVp" value="p6_Kozak-ATG.gb" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
65 <element name="p16_bGHpolyA" value="p4_Kt-L7Ae-Weiss.gb" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
66 <element name="p18_CMVp" value="HC_Amp_ccdB.gb" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
67 </conditional>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
68 </param>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
69 <conditional name="json_use">
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
70 <param name='use_json_paramers' value='false' />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
71 <param name="table" value="sample" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
72 <param name="sequence_column" value="sequence" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
73 <param name="annotation_column" value="annotation" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
74 <param name="fragment_column" value="fragment" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
75 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
76 <param name="execution_enable" value="false" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
77 </conditional>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
78 <param name="use_json_paramers" value='true'/>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
79 <output name="output" file="test_raport.txt" ftype="txt" >
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
80 <assert_contents>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
81 <has_n_lines n="0" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
82 </assert_contents>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
83 </output>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
84 <output name="json_output">
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
85 <assert_contents>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
86 <has_n_lines n="8" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
87 </assert_contents>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
88 </output>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
89 </test>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
90 <!--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 -->
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
91 <test expect_num_outputs="1">
1
3daf04425ea1 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents: 0
diff changeset
92 <param name="genbank_files">
3daf04425ea1 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents: 0
diff changeset
93 <collection type="list">
3daf04425ea1 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents: 0
diff changeset
94 <element name="p7_L7Ae-Weiss" value="p7_L7Ae-Weiss.gb" />
3daf04425ea1 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents: 0
diff changeset
95 <element name="p7_gfp_sequence" value="p6_Nt-IgKLsequence.gb" />
3daf04425ea1 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents: 0
diff changeset
96 <element name="p14_CMVp" value="p6_Kozak-ATG.gb" />
3daf04425ea1 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents: 0
diff changeset
97 <element name="p16_bGHpolyA" value="p4_Kt-L7Ae-Weiss.gb" />
3daf04425ea1 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents: 0
diff changeset
98 <element name="p18_CMVp" value="HC_Amp_ccdB.gb" />
3daf04425ea1 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents: 0
diff changeset
99 </collection>
3daf04425ea1 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents: 0
diff changeset
100 </param>
2
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
101 <conditional name="json_use">
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
102 <param name="use_json_paramers" value='true'/>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
103 <param name="json_conf" value="test-JSON_arg_block.json" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
104 </conditional>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
105 <param name="json_generating" value='false'/>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
106 <param name="json_conf" value="test-JSON_arg_block.json" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
107 <output name="output" file="test_raport.txt" ftype="txt" >
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
108 <assert_contents>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
109 <has_n_lines n="0" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
110 </assert_contents>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
111 </output>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
112 </test>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
113 <!--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)-->
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
114 <!--test DB config in the tool -->
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
115 <test expect_num_outputs="2">
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
116 <param name="genbank_files">
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
117 <collection type="list">
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
118 <element name="p7_L7Ae-Weiss" value="p7_L7Ae-Weiss.gb" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
119 <element name="p7_gfp_sequence" value="p6_Nt-IgKLsequence.gb" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
120 <element name="p14_CMVp" value="p6_Kozak-ATG.gb" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
121 <element name="p16_bGHpolyA" value="p4_Kt-L7Ae-Weiss.gb" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
122 <element name="p18_CMVp" value="HC_Amp_ccdB.gb" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
123 </collection>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
124 </param>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
125 <conditional name="json_use">
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
126 <param name="use_json_paramers" value='false'/>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
127 <param name="table" value="sample" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
128 <param name="sequence_column" value="sequence" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
129 <param name="annotation_column" value="annotation" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
130 <param name="fragment_column" value="fragment" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
131 <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
132 <param name="execution_enable" value="true" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
133 </conditional>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
134 <param name="use_json_paramers" value='true'/>
1
3daf04425ea1 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents: 0
diff changeset
135 <output name="output" file="test_raport.txt" ftype="txt" >
3daf04425ea1 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents: 0
diff changeset
136 <assert_contents>
3daf04425ea1 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents: 0
diff changeset
137 <has_n_lines n="5" />
3daf04425ea1 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents: 0
diff changeset
138 <has_line_matching expression="p7_L7Ae-Weiss" />
3daf04425ea1 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents: 0
diff changeset
139 <has_line_matching expression="p6_Nt-IgKLsequence" />
3daf04425ea1 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents: 0
diff changeset
140 <has_line_matching expression="p6_Kozak-ATG" />
3daf04425ea1 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents: 0
diff changeset
141 <has_line_matching expression="p4_Kt-L7Ae-Weiss" />
3daf04425ea1 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents: 0
diff changeset
142 <has_line_matching expression="HC_Amp_ccdB" />
3daf04425ea1 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents: 0
diff changeset
143 </assert_contents>
3daf04425ea1 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents: 0
diff changeset
144 </output>
2
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
145 <output name="json_output">
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
146 <assert_contents>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
147 <has_n_lines n="8" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
148 </assert_contents>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
149 </output>
1
3daf04425ea1 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents: 0
diff changeset
150 </test>
2
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
151 <!--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)-->
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
152 <test expect_num_outputs="1">
0
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
153 <param name="genbank_files">
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
154 <collection type="list">
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
155 <element name="p7_L7Ae-Weiss" value="p7_L7Ae-Weiss.gb" />
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
156 <element name="p7_gfp_sequence" value="p6_Nt-IgKLsequence.gb" />
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
157 <element name="p14_CMVp" value="p6_Kozak-ATG.gb" />
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
158 <element name="p16_bGHpolyA" value="p4_Kt-L7Ae-Weiss.gb" />
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
159 <element name="p18_CMVp" value="HC_Amp_ccdB.gb" />
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
160 </collection>
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
161 </param>
2
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
162 <conditional name="json_use">
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
163 <param name="use_json_paramers" value='true'/>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
164 <param name="json_conf" value="test-JSON_arg.json" />
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
165 </conditional>
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
166 <param name="json_generating" value='false'/>
0
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
167 <output name="output" file="test_raport.txt" ftype="txt" >
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
168 <assert_contents>
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
169 <has_n_lines n="5" />
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
170 <has_line_matching expression="p7_L7Ae-Weiss" />
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
171 <has_line_matching expression="p6_Nt-IgKLsequence" />
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
172 <has_line_matching expression="p6_Kozak-ATG" />
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
173 <has_line_matching expression="p4_Kt-L7Ae-Weiss" />
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
174 <has_line_matching expression="HC_Amp_ccdB" />
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
175 </assert_contents>
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
176 </output>
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
177 </test>
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
178 </tests>
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
179
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
180 <help><![CDATA[
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
181 Save Sequence Data In DB
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
182 ========================
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
183
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
184 Implemented a system to save GenBank (.gb) files in an accessible DB, based on a connection via URI requests.
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
185
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
186 **Parameters**:
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
187 ---------------
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
188 * **GenBank File(s)**: List of GenBaks files.
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
189 * **DB Table Name**: Name of the target table in the PostgreSQL database.
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
190 * **DB Column Contains Sequence For ganbank File**: Column storing sequence data, expected to start with "ORIGIN".
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
191 * **DB Column Contains Annotation For Ganbank File**: Column containing annotation data, to save al part before "ORIGIN" in the .gb file.
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
192 * **DB IDs Column Name**: Column holding the unique fragment IDs.
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
193 * **DB Connection URI**: URI used to connect to the database (e.g., postgresql://postgres:pass@localhost:5432/test_fragments_db).
1
3daf04425ea1 planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents: 0
diff changeset
194 * **Send Requenst to DB**: Enable or Desable the interaction with the DB (can be usefull in workflows).
0
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
195 * **DB config as a json file**: JSON file contains the DB configuration:
2
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
196 - "table": will be the key to the table name.
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
197 - "sequence_column": will be the key to the sequence column.
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
198 - "annotation_column": will be the key to the annotation column.
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
199 - "fragment_column": will be the key to the fragment column.
dad2c4c3450a planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit db4ac861e1d03fcdfe94321d858839124e493930-dirty
tduigou
parents: 1
diff changeset
200 - "db_uri": will be the key to the URI.
0
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
201 - "execution": It is the key to execute or block the tool during a workflow ("True" or "False").
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
202 ]]></help>
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
203 <citations>
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
204 <citation type="bibtex">
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
205 @unpublished{seq_to_db
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
206 author = {Ramiz Khaled},
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
207 title = {{seq_to_db}},
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
208 url = {https://github.com/brsynth/},
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
209 }
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
210 </citation>
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
211 </citations>
9f845ccb1a9f planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit 3401816c949b538bd9c67e61cbe92badff6a4007-dirty
tduigou
parents:
diff changeset
212 </tool>