changeset 12:3af838dc0637 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 85f81cd54f7bd9e2e8b6f0ba1260520ad24d28cd

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu May 15 12:51:53 2025 +0000
@@ -0,0 +1,9 @@
+<macros>
+    <xml name="columns" tokens="header">
+        <param name="fdr_col" type="data_column" use_header_names="@HEADER@" data_ref="input" label="FDR (adjusted P value) column number" />
+        <param name="pval_col" type="data_column" use_header_names="@HEADER@" data_ref="input" label="P value (raw) column number" />
+        <param name="lfc_col" type="data_column" use_header_names="@HEADER@" data_ref="input" label="Log Fold Change column number" />
+        <param name="label_col" type="data_column" use_header_names="@HEADER@" data_ref="input" label="Labels column number" />
+        <param name="shape_col" type="data_column" use_header_names="@HEADER@" data_ref="input" label="Categories that can be used to plot different shapes or facet (useful if multivariable associations are investigated)" optional="true" />
+    </xml>
+</macros>
\ No newline at end of file

--- a/volcanoplot.xml	Wed Jan 29 10:37:54 2025 +0000
+++ b/volcanoplot.xml	Thu May 15 12:51:53 2025 +0000
@@ -1,13 +1,20 @@
-<tool id="volcanoplot" name="Volcano Plot" version="0.0.7" profile="20.09">
+<tool id="volcanoplot" name="Volcano Plot" version="@TOOL_VERSION@+galaxy0" profile="20.09">
     <description>create a volcano plot</description>
+    <macros>
+        <import>macros.xml</import>
+        <token name="@TOOL_VERSION@">3.3.3</token>
+    </macros>
+
     <edam_topics>
         <edam_topic>topic_0092</edam_topic>
     </edam_topics>
+
     <edam_operations>
         <edam_operation>operation_0337</edam_operation>
     </edam_operations>
+
     <requirements>
-        <requirement type="package" version="3.3.3">r-ggplot2</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">r-ggplot2</requirement>
         <requirement type="package" version="0.9.1">r-ggrepel</requirement>
         <requirement type="package" version="1.0.6">r-dplyr</requirement>
     </requirements>
@@ -203,16 +210,23 @@
 </configfiles>
     <inputs>
         <param name="input" type="data" format="tabular" label="Specify an input file" />
-        <param name="header" type="select" label="File has header?" help="Does the differentially expressed results file contain a header row. The tool can auto-detect by checking if the first row in the P value column is a number or not. Default: Auto-detect">
-            <option value="auto" selected="True">Auto-detect</option>
-            <option value="yes">Yes</option>
-            <option value="no">No</option>
-        </param>
-        <param name="fdr_col" type="data_column" data_ref="input" label="FDR (adjusted P value) column number" />
-        <param name="pval_col" type="data_column" data_ref="input" label="P value (raw) column number" />
-        <param name="lfc_col" type="data_column" data_ref="input" label="Log Fold Change column number" />
-        <param name="label_col" type="data_column" data_ref="input" label="Labels column number" />
-        <param name="shape_col" type="data_column" data_ref="input" label="Categories that can be used to plot different shapes or facet (useful if multivariable associations are investigated)" optional="true" />
+        <conditional name="with_header">
+            <param name="header" type="select" label="File has header?" refresh_on_change="true" help="Does the differentially expressed results file contain a header row. The tool can auto-detect by checking if the first row in the P value column is a number or not. Default: Auto-detect">
+                <option value="auto" selected="True">Auto-detect</option>
+                <option value="yes">Yes</option>
+                <option value="no">No</option>
+            </param>
+            <when value="auto">
+                <expand macro="columns" header="false"/>
+            </when>
+            <when value="yes">
+                <expand macro="columns" header="true"/>
+            </when>
+            <when value="no">
+                <expand macro="columns" header="false"/>
+            </when>
+        </conditional>
+
         <param name="shape_or_facet" type="select" label="Display categories by:" help="Choose whether to display categories by faceting the plot or using shape." optional="true">
             <option value="facet">Facet</option>
             <option value="shape">Shape</option>