diff FROGS_FUNC.xml @ 0:c5fd7b97c2a4 draft default tip

planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 78ca62b54aee22893d278d9c3d495527be405f8a

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FROGS_FUNC.xml	Wed Feb 04 13:17:34 2026 +0000
@@ -0,0 +1,90 @@
+<tool id="FROGS_Func" name="FROGS Func" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="24.0">
+    <description>Prediction of functional abundances using marker gene sequences</description>
+    <macros>
+        <import>frogs_func_macros.xml</import>
+        <import>picrust2_placeseq_and_copynumber_macros.xml</import>
+        <import>picrust2_functions_macros.xml</import>
+        <import>picrust2_pathways_macros.xml</import>
+    </macros>
+
+    <expand macro="frogs_func_requirements" />
+
+    <command detect_errors="exit_code"><![CDATA[
+        #if $frogs_func_tools.tool_name == "picrust2_placeseq_and_copynumber"
+            @PICRUST2_PLACESEQ_AND_COPYNUMBER_CMD_LINE@
+
+        #elif $frogs_func_tools.tool_name == "picrust2_functions"
+            @PICRUST2_FUNCTIONS_CMD_LINE@
+
+        #elif $frogs_func_tools.tool_name == "picrust2_pathways"
+            @PICRUST2_PATHWAYS_CMD_LINE@
+        #end if
+    ]]>
+    </command>
+    
+    <inputs>
+        <conditional name="frogs_func_tools">
+            <param name="tool_name" type="select" display="radio" label="Select a tool from the FROGS Func suite to run your analysis.">
+                <option value="" selected="true">-- Please select a tool --</option>
+                <option value="picrust2_placeseq_and_copynumber"> Tool 1: sequence placement and gene copy number estimation (PICRUSt2)</option>
+                <option value="picrust2_functions">Tool 2: functional abundance estimation (PICRUSt2)</option>
+                <option value="picrust2_pathways">Tool 3: pathway abundance estimation (PICRUSt2)</option>
+            </param>
+            <when value=""/>
+            <!-- ##################### picrust2_placeseq_and_copynumber  ##################### -->
+            <when value="picrust2_placeseq_and_copynumber">
+                <expand macro="picrust2_placeseq_and_copynumber_inputs" />
+            </when>
+            <!-- ##################### picrust2_functions  ##################### -->
+            <when value="picrust2_functions">
+                <expand macro="picrust2_functions_inputs" />
+            </when>
+            <!-- ##################### picrust2_pathways  ##################### -->
+            <when value="picrust2_pathways">
+                <expand macro="picrust2_pathways_inputs" />
+            </when>
+        </conditional>
+    </inputs>
+    
+    <outputs>
+        <expand macro="frogs_func_outputs" />
+    </outputs>
+    
+    <tests>
+        <!-- ##################### 1 picrust2_placeseq_and_copynumber ##################### -->
+        <test expect_num_outputs="7">
+            <conditional name="frogs_func_tools">
+                <param name="tool_name" value="picrust2_placeseq_and_copynumber"/>
+                <expand macro="picrust2_placeseq_and_copynumber_test_input"/>
+            </conditional>
+            <expand macro="picrust2_placeseq_and_copynumber_test_output"/>
+        </test>
+        <!-- ##################### 2 picrust2_functions ##################### -->
+        <test expect_num_outputs="8">
+            <conditional name="frogs_func_tools">
+                <param name="tool_name" value="picrust2_functions"/>
+                <expand macro="picrust2_functions_test_input"/>
+            </conditional>
+            <expand macro="picrust2_functions_test_output"/>
+        </test>        
+        <!-- ##################### 3 picrust2_pathways ##################### -->
+        <test expect_num_outputs="2">
+            <conditional name="frogs_func_tools">
+                <param name="tool_name" value="picrust2_pathways"/>
+                <expand macro="picrust2_pathways_test_input"/>
+            </conditional>
+            <expand macro="picrust2_pathways_test_output"/>
+        </test>    
+    </tests>
+
+    <help><![CDATA[
+    For more information and detailed documentation, visit the FROGS website https://frogs.inrae.fr.
+    ]]>
+    </help>
+
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btx791</citation>
+        <citation type="doi">10.1093/bib/bbab318</citation>
+    </citations>
+
+</tool>