diff json_db_config_generating_boolean.xml @ 0:1a766d8d3883 draft

planemo upload for repository https://github.com/brsynth commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/json_db_config_generating_boolean.xml	Fri Jul 11 10:10:16 2025 +0000
@@ -0,0 +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>
+    <macros>
+        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@TOOL_VERSION@">0.1.0</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'
+    ]]></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' />
+    </inputs>   
+    <outputs>
+        <data name="output_workflow" format="json" label="workflow param"/>
+        <data name="output_user" format="json" label="user_workflow param"/>
+    </outputs>
+    <tests>
+        <!--distribute_json is false-->
+        <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">
+                <assert_contents>
+                    <has_n_lines n="17" />
+                </assert_contents>
+            </output>
+            <output name="output_workflow">
+                <assert_contents>
+                    <has_n_lines n="0" />
+                </assert_contents>
+            </output>
+        </test>
+        <!--distribute_json is true -->
+        <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">
+                <assert_contents>
+                    <has_n_lines n="17" />
+                </assert_contents>
+            </output>
+            <output name="output_user">
+                <assert_contents>
+                    <has_n_lines n="0" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+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.
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+            @unpublished{json_db_config_generating
+                author = {Ramiz Khaled},
+                title = {{json_db_config_generating}},
+                url = {https://github.com/brsynth/},
+            }
+        </citation>
+    </citations>
+</tool>
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