--- a/seq_to_db.xml	Thu Jun 12 09:04:14 2025 +0000
+++ b/seq_to_db.xml	Wed Jul 23 09:44:33 2025 +0000
@@ -1,8 +1,8 @@
 <tool id="seq_to_db" name="Save Sequence Data In DB" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
     <description>Save fragment's sequence in an accessible database and import it from .gb files</description>
     <macros>
-        <token name="@VERSION_SUFFIX@">1</token>
-        <token name="@TOOL_VERSION@">0.2.0</token>
+        <token name="@VERSION_SUFFIX@">2</token>
+        <token name="@TOOL_VERSION@">0.3.0</token>
     </macros>
     <requirements>
         <requirement type="package" version="2.2.3">pandas</requirement>
@@ -11,37 +11,84 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #set genbank_file_paths = ','.join([str(f) for f in $genbank_files])
-        #set $file_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $genbank_files])
+        #set file_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $genbank_files])
         python '$__tool_directory__/save_to_db.py'
-            --input '$genbank_file_paths' 
-            --sequence_column '$sequence_column'
-            --annotation_column '$annotation_column'
-            --db_uri '$db_uri' 
-            --table '$table' 
-            --fragment_column '$fragment_column'
+            --input '$genbank_file_paths'
+            --use_json_paramers '$json_use.use_json_paramers'
+            #if not $json_use.use_json_paramers:
+                --sequence_column '$json_use.sequence_column'
+                --annotation_column '$json_use.annotation_column'
+                --db_uri '$json_use.db_uri' 
+                --table '$json_use.table' 
+                --fragment_column '$json_use.fragment_column'
+                --execution_enable '$json_use.execution_enable'
+            #else:
+                --json_conf '$json_use.json_conf'
+            #end if
             --output '$output'
             --file_name_mapping '$file_name_mapping'
-            --json_conf '$json_conf'
-            --execution_enable '$execution_enable'
+            --json_generating '$json_generating'
+            --json_output '$json_output'
     ]]></command>
-    <inputs>
+        <inputs>
         <param name="genbank_files" type="data_collection" collection_type="list" format="genbank" label="GenBank File(s)"/>
-        <param name="table" type="text" label="DB Table Name" optional="true" help="It can be extracted from JSON file -key:'JSON_table'-" />
-        <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'-" />
-        <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'-" />
-        <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'-" />
-        <param name="db_uri" type="text" label="DB Connection URI" help="postgresql://(user_name or container_name):password@host:port/path/to/database (It can be extracted from JSON file -key:'JSON_db_uri'-)" optional="true" />
-        <section name='adv' title='Advance' expanded='false'>
-            <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)" />
-            <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" />
-        </section>
+        <conditional name="json_use">
+            <param name="use_json_paramers" type="boolean" checked='false' label="Use parameters from JSON" help="extract parameters from json file" />
+            <when value="false">
+                <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)" />
+                <param name="table" type="text" label="DB Table Name" optional="true" help="It can be extracted from JSON file -key:'table'-" />
+                <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'-" />
+                <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'-" />
+                <param name="fragment_column" type="text" label="DB IDs Column Name" optional="true" help="It can be extracted from JSON file -key:'fragment_column'-" />
+                <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" />
+            </when>
+            <when value="true">
+                <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" />
+            </when>
+        </conditional>
+        <param name="json_generating" type="boolean" checked='true' label="Generat Parameters in JSON" help="generat parameters in json file" />
     </inputs>   
     <outputs>
         <data name="output" format="txt" label="saving report" />
+        <data name="json_output" format="json" label="seq_to_db_param">
+            <filter>json_generating == True</filter>
+        </data>
     </outputs>
     <tests>
         <!--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 -->
-        <test> 
+        <test expect_num_outputs="2"> 
+            <param name="genbank_files">
+                <conditional type="list">
+                    <element name="p7_L7Ae-Weiss" value="p7_L7Ae-Weiss.gb" />
+                    <element name="p7_gfp_sequence" value="p6_Nt-IgKLsequence.gb" />
+                    <element name="p14_CMVp" value="p6_Kozak-ATG.gb" />
+                    <element name="p16_bGHpolyA" value="p4_Kt-L7Ae-Weiss.gb" />
+                    <element name="p18_CMVp" value="HC_Amp_ccdB.gb" />
+                </conditional>
+            </param>
+            <conditional name="json_use">
+                <param name='use_json_paramers' value='false' />
+                <param name="table" value="sample" />
+                <param name="sequence_column" value="sequence" />
+                <param name="annotation_column" value="annotation" />
+                <param name="fragment_column" value="fragment" />
+                <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
+                <param name="execution_enable" value="false" />
+            </conditional>
+            <param name="use_json_paramers" value='true'/>
+            <output name="output" file="test_raport.txt" ftype="txt" >
+                <assert_contents>
+                     <has_n_lines n="0" />
+                </assert_contents>
+            </output>
+            <output name="json_output">
+                <assert_contents>
+                     <has_n_lines n="8" />
+                </assert_contents>
+            </output>
+        </test>
+        <!--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 -->
+        <test expect_num_outputs="1"> 
             <param name="genbank_files">
                 <collection type="list">
                     <element name="p7_L7Ae-Weiss" value="p7_L7Ae-Weiss.gb" />
@@ -51,12 +98,40 @@
                     <element name="p18_CMVp" value="HC_Amp_ccdB.gb" />
                 </collection>
             </param>
-            <param name="table" value="sample" />
-            <param name="sequence_column" value="sequence" />
-            <param name="annotation_column" value="annotation" />
-            <param name="fragment_column" value="fragment" />
-            <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
-            <param name="adv|execution_enable" value="false" />
+            <conditional name="json_use">
+                <param name="use_json_paramers" value='true'/>
+                <param name="json_conf" value="test-JSON_arg_block.json" />
+            </conditional>
+            <param name="json_generating" value='false'/>
+            <param name="json_conf" value="test-JSON_arg_block.json" />
+            <output name="output" file="test_raport.txt" ftype="txt" >
+                <assert_contents>
+                     <has_n_lines n="0" />
+                </assert_contents>
+            </output>
+        </test>
+        <!--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)-->
+        <!--test DB config in the tool -->
+        <test expect_num_outputs="2"> 
+            <param name="genbank_files">
+                <collection type="list">
+                    <element name="p7_L7Ae-Weiss" value="p7_L7Ae-Weiss.gb" />
+                    <element name="p7_gfp_sequence" value="p6_Nt-IgKLsequence.gb" />
+                    <element name="p14_CMVp" value="p6_Kozak-ATG.gb" />
+                    <element name="p16_bGHpolyA" value="p4_Kt-L7Ae-Weiss.gb" />
+                    <element name="p18_CMVp" value="HC_Amp_ccdB.gb" />
+                </collection>
+            </param>
+            <conditional name="json_use">
+                <param name="use_json_paramers" value='false'/>
+                <param name="table" value="sample" />
+                <param name="sequence_column" value="sequence" />
+                <param name="annotation_column" value="annotation" />
+                <param name="fragment_column" value="fragment" />
+                <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
+                <param name="execution_enable" value="true" />
+            </conditional>
+            <param name="use_json_paramers" value='true'/>
             <output name="output" file="test_raport.txt" ftype="txt" >
                 <assert_contents>
                      <has_n_lines n="5" />
@@ -67,9 +142,14 @@
                      <has_line_matching expression="HC_Amp_ccdB" />
                 </assert_contents>
             </output>
+            <output name="json_output">
+                <assert_contents>
+                     <has_n_lines n="8" />
+                </assert_contents>
+            </output>
         </test>
-        <!--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 -->
-        <test> 
+        <!--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)-->
+        <test expect_num_outputs="1"> 
             <param name="genbank_files">
                 <collection type="list">
                     <element name="p7_L7Ae-Weiss" value="p7_L7Ae-Weiss.gb" />
@@ -79,58 +159,11 @@
                     <element name="p18_CMVp" value="HC_Amp_ccdB.gb" />
                 </collection>
             </param>
-            <param name="adv|json_conf" value="test-JSON_arg_block.json" />
-            <output name="output" file="test_raport.txt" ftype="txt" >
-                <assert_contents>
-                     <has_n_lines n="5" />
-                     <has_line_matching expression="p7_L7Ae-Weiss" />
-                     <has_line_matching expression="p6_Nt-IgKLsequence" />
-                     <has_line_matching expression="p6_Kozak-ATG" />
-                     <has_line_matching expression="p4_Kt-L7Ae-Weiss" />
-                     <has_line_matching expression="HC_Amp_ccdB" />
-                </assert_contents>
-            </output>
-        </test>
-        <!--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)-->
-        <!--test DB config in the tool -->
-        <test> 
-            <param name="genbank_files">
-                <collection type="list">
-                    <element name="p7_L7Ae-Weiss" value="p7_L7Ae-Weiss.gb" />
-                    <element name="p7_gfp_sequence" value="p6_Nt-IgKLsequence.gb" />
-                    <element name="p14_CMVp" value="p6_Kozak-ATG.gb" />
-                    <element name="p16_bGHpolyA" value="p4_Kt-L7Ae-Weiss.gb" />
-                    <element name="p18_CMVp" value="HC_Amp_ccdB.gb" />
-                </collection>
-            </param>
-            <param name="table" value="sample" />
-            <param name="sequence_column" value="sequence" />
-            <param name="annotation_column" value="annotation" />
-            <param name="fragment_column" value="fragment" />
-            <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
-            <output name="output" file="test_raport.txt" ftype="txt" >
-                <assert_contents>
-                     <has_n_lines n="5" />
-                     <has_line_matching expression="p7_L7Ae-Weiss" />
-                     <has_line_matching expression="p6_Nt-IgKLsequence" />
-                     <has_line_matching expression="p6_Kozak-ATG" />
-                     <has_line_matching expression="p4_Kt-L7Ae-Weiss" />
-                     <has_line_matching expression="HC_Amp_ccdB" />
-                </assert_contents>
-            </output>
-        </test>
-        <!--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)-->
-        <test> 
-            <param name="genbank_files">
-                <collection type="list">
-                    <element name="p7_L7Ae-Weiss" value="p7_L7Ae-Weiss.gb" />
-                    <element name="p7_gfp_sequence" value="p6_Nt-IgKLsequence.gb" />
-                    <element name="p14_CMVp" value="p6_Kozak-ATG.gb" />
-                    <element name="p16_bGHpolyA" value="p4_Kt-L7Ae-Weiss.gb" />
-                    <element name="p18_CMVp" value="HC_Amp_ccdB.gb" />
-                </collection>
-            </param>
-            <param name="adv|json_conf" value="test-JSON_arg.json" />
+            <conditional name="json_use">
+                <param name="use_json_paramers" value='true'/>
+                <param name="json_conf" value="test-JSON_arg.json" />
+            </conditional>
+            <param name="json_generating" value='false'/>
             <output name="output" file="test_raport.txt" ftype="txt" >
                 <assert_contents>
                      <has_n_lines n="5" />
@@ -160,11 +193,11 @@
 * **DB Connection URI**: URI used to connect to the database (e.g., postgresql://postgres:pass@localhost:5432/test_fragments_db).
 * **Send Requenst to DB**: Enable or Desable the interaction with the DB (can be usefull in workflows).
 * **DB config as a json file**: JSON file contains the DB configuration:
-    - "JSON_table": will be the key to the table name.
-    - "JSON_sequence_column":  will be the key to the sequence column.
-    - "JSON_annotation_column":  will be the key to the annotation column.
-    - "JSON_fragment_column": will be the key to the fragment column.
-    - "JSON_db_uri": will be the key to the URI.
+    - "table": will be the key to the table name.
+    - "sequence_column":  will be the key to the sequence column.
+    - "annotation_column":  will be the key to the annotation column.
+    - "fragment_column": will be the key to the fragment column.
+    - "db_uri": will be the key to the URI.
     - "execution": It is the key to execute or block the tool during a workflow ("True" or "False").
     ]]></help>
     <citations>