diff json_db_config_generating_boolean.xml @ 1:34135dac85b0 draft default tip

planemo upload for repository https://github.com/brsynth commit d8cc8b87fdb0374745b5420f2da7f08ae905c222-dirty

--- a/json_db_config_generating_boolean.xml	Fri Jul 11 10:10:16 2025 +0000
+++ b/json_db_config_generating_boolean.xml	Wed Jul 16 14:28:21 2025 +0000
@@ -1,58 +1,76 @@
-<tool id="parameters_maystro" name="Parameters Maystro" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
-    <description>Store parameters of tools in a workflow to be used again</description>
+<tool id="parameters_maystro" name="Workflow-0 Parameters Maystro" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
+    <description>Store parameters of workflow-0 to be used again</description>
     <macros>
-        <token name="@VERSION_SUFFIX@">1</token>
-        <token name="@TOOL_VERSION@">0.1.0</token>
+        <token name="@VERSION_SUFFIX@">3</token>
+        <token name="@TOOL_VERSION@">1.1.0</token>
     </macros>
     <command detect_errors="exit_code"><![CDATA[
-        #set $json_files = ' '.join(['"%s"' % file for file in $json_from_workflow])
-        #set $json_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $json_from_workflow])
-        python '$__tool_directory__/maystro.py'
-            --distribute_json '$distribute_json'
-            --json_from_workflow $json_files
-            --json_from_user '$json_from_user'
-            --json_name_mapping $json_name_mapping
-            --output_workflow '$output_workflow'
-            --output_user '$output_user' && echo 'DEBUB' && cat '$output_user'
+    #if $user_json and str($user_json) != 'None':
+        cp '$user_json' '$output_json'
+    #else
+        python3 -c "import json; params = {
+        'avoid_patterns': '$avoid_patterns',
+        'hairpin_constraints': '$hairpin_constraints',
+        'gc_constraints': '$gc_constraints',
+        'kmer_size': '$kmer_size',
+        'execution': '$execution',
+        'db_uri': '$db_uri',
+        'table': '$table_name',
+        'fragment_column': '$fragment_column',
+        'sequence_column': '$sequence_column',
+        'annotation_column': '$annotation_column'
+        }; f = open('$output_json', 'w'); json.dump(params, f, indent=4); f.close()" && echo DEBG && cat '$output_json'
+    #end if
+    && echo DEBG && cat '$output_json'
     ]]></command>
     <inputs>
-        <param name="distribute_json" type="boolean" label="Input Your Parameters As JSON" checked ='false' help="If True user should set workflow parameters as json file" />
-        <param name="json_from_workflow" type="data" format="json" multiple="true" optional="true" help='Only if Input Your Parameters As JSON is FALSE' />
-        <param name="json_from_user" type="data" format="json" optional="true" help='Only if Input Your Parameters As JSON is TRUE' />
+        <param name="avoid_patterns" type="text" area="true" optional="true" label="Avoid Patterns (one per line)" />
+        <param name="hairpin_constraints" type="text" area="true" label="Hairpins Constraints" optional="true" help="e.g. (you can add others Hairpins Constraints on a new line): stem_size=20, hairpin_window=200"/>
+        <param name="gc_constraints" type="text" area="true" label="Enforce GC Content Constraints" optional="true" help="e.g. (you can add others Enforce GC Content Constraints on a new line): mini=0.3, maxi=0.7, window=100"/>
+        <param name="kmer_size" type="integer" label="K-mer Uniqueness Size" value="" optional="true" help="e.g.: 15"/>
+        <param name="execution" type="boolean" label="Save To DB ?" checked ='false' optional="true" help="If True data will be saved in the DB" />
+        <param name="db_uri" type="text" optional="true" help='Only if Input Your Parameters As JSON is FALSE' />
+        <param name="table_name" type="text" optional="true" help='table name in DB' />
+        <param name="fragment_column" type="text" optional="true" help='Fragmnet column in DB' />
+        <param name="sequence_column" type="text" optional="true" help='Sequence column in DB' />
+        <param name="annotation_column" type="text" optional="true" help='Annotation column in DB' />
+        <param name="user_json" type="data" format="json" optional="true" help='Only if Input Your Parameters As JSON is TRUE' />
     </inputs>   
     <outputs>
-        <data name="output_workflow" format="json" label="workflow param"/>
-        <data name="output_user" format="json" label="user_workflow param"/>
+        <data name="output_json" format="json" label="Workflow-0 Parameters"/>
     </outputs>
     <tests>
-        <!--distribute_json is false-->
+        <!--manual parameters set-->
         <test> 
-            <param name="distribute_json" value='false'/>
-            <param name="json_from_workflow" value="seq_from_db_param.json,seq_to_db_param.json"/>
-            <output name="output_user">
+            <param name="avoid_patterns" value="BsaI_site
+            BsmBI_site
+            BbsI_site
+            SapI_site
+            8x1mer
+            5x3mer
+            9x2mer" />
+            <param name="hairpin_constraints" value='stem_size=20, hairpin_window=200'/>
+            <param name="gc_constraints" value="mini=0.3, maxi=0.7, window=100
+            mini=0.1, maxi=0.9, window=100"/>
+            <param name="kmer_size" value="15" />
+            <param name="execution" value="true" />
+            <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />
+            <param name="table_name" value="sample" />
+            <param name="fragment_column" value="fragment" />
+            <param name="sequence_column" value="sequence" />
+            <param name="annotation_column" value="annotation" />
+            <output name="output_json">
                 <assert_contents>
-                    <has_n_lines n="17" />
-                </assert_contents>
-            </output>
-            <output name="output_workflow">
-                <assert_contents>
-                    <has_n_lines n="0" />
+                    <has_n_lines n="12" />
                 </assert_contents>
             </output>
         </test>
-        <!--distribute_json is true -->
+        <!--JSON parameters set-->
         <test> 
-            <param name="distribute_json" value='true'/>
-            <param name="json_from_workflow" value="seq_from_db_param.json,seq_to_db_param.json"/>
-            <param name="json_from_user" value='merged_test.json'/>
-            <output name="output_workflow">
+            <param name="user_json" value='test_json.json'/>
+            <output name="output_json">
                 <assert_contents>
-                    <has_n_lines n="17" />
-                </assert_contents>
-            </output>
-            <output name="output_user">
-                <assert_contents>
-                    <has_n_lines n="0" />
+                    <has_n_lines n="12" />
                 </assert_contents>
             </output>
         </test>
@@ -61,8 +79,8 @@
 Parameters Maystro
 ===================
 
-Store and Generate a JSON file to be used as a workflow configuration. This JSON file can later be used to pass workflow parameters
-This tool is recieve parameters from tools in workflow and return them as a JSON file that can be used later to pass thos parameters again.
+Store and Generate a JSON file to be used as workflow-0 configuration. This JSON file can later be used as input to pass workflow-0 parameters
+
     ]]></help>
     <citations>
         <citation type="bibtex">