From 6616f67844f7913a3e0bb1699bf326ebf771f84f Mon Sep 17 00:00:00 2001
From: Helge Hecht <helge.hecht@recetox.muni.cz>
Date: Thu, 23 Jan 2025 08:52:38 +0000
Subject: [PATCH 1/3] Add "use_header_names" option to histogram

---
 tools/histogram/histogram2.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/histogram/histogram2.xml b/tools/histogram/histogram2.xml
index 56d22742..5f3d8cbe 100644
--- a/tools/histogram/histogram2.xml
+++ b/tools/histogram/histogram2.xml
@@ -1,4 +1,4 @@
-<tool id="histogram_rpy" name="Histogram" version="1.0.4">
+<tool id="histogram_rpy" name="Histogram" version="1.0.5">
   <description>of a numeric column</description>
   <requirements>
     <requirement type="package" version="3.3.2">rpy2</requirement>
@@ -17,7 +17,7 @@ python '$__tool_directory__/histogram.py'
 </command>
   <inputs>
     <param name="input" type="data" format="tabular" label="Dataset" help="Dataset missing? See TIP below"/>
-    <param name="numerical_column" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" />
+    <param name="numerical_column" type="data_column" data_ref="input" numerical="True" use_header_names="true" label="Numerical column for x axis" />
     <param name="breaks" type="integer" value="0" label="Number of breaks (bars)"/>
     <param name="title" type="text" value="Histogram" label="Plot title"/>
     <param name="xlab" type="text" value="V1" label="Label for x axis"/>

From 85da33bfe0843bdb6a1a96af3585871083e83d56 Mon Sep 17 00:00:00 2001
From: hechth <helge.hecht@recetox.muni.cz>
Date: Mon, 3 Feb 2025 12:08:12 +0100
Subject: [PATCH 2/3] fixed linting

---
 tools/histogram/.shed.yml      | 1 +
 tools/histogram/histogram2.xml | 3 +++
 2 files changed, 4 insertions(+)

diff --git a/tools/histogram/.shed.yml b/tools/histogram/.shed.yml
index 990968cb..4470a935 100644
--- a/tools/histogram/.shed.yml
+++ b/tools/histogram/.shed.yml
@@ -7,4 +7,5 @@ long_description: |
 name: histogram
 owner: devteam
 remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram
+homepage_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram
 type: unrestricted
diff --git a/tools/histogram/histogram2.xml b/tools/histogram/histogram2.xml
index 5f3d8cbe..d2612f64 100644
--- a/tools/histogram/histogram2.xml
+++ b/tools/histogram/histogram2.xml
@@ -84,4 +84,7 @@ This tool computes a histogram of the numerical values in a column of a dataset.
 .. image:: histogram2.png
 
 </help>
+<citations>
+  <citation type="doi">10.1145/3386334</citation>
+</citations>
 </tool>

From 07b3f13ec51bb60ff370f8eb89fbdc38cc1b5615 Mon Sep 17 00:00:00 2001
From: hechth <helge.hecht@recetox.muni.cz>
Date: Tue, 4 Feb 2025 11:02:22 +0100
Subject: [PATCH 3/3] added select to choose column

---
 tools/histogram/histogram2.xml | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/tools/histogram/histogram2.xml b/tools/histogram/histogram2.xml
index d2612f64..885fc1ea 100644
--- a/tools/histogram/histogram2.xml
+++ b/tools/histogram/histogram2.xml
@@ -17,7 +17,18 @@ python '$__tool_directory__/histogram.py'
 </command>
   <inputs>
     <param name="input" type="data" format="tabular" label="Dataset" help="Dataset missing? See TIP below"/>
-    <param name="numerical_column" type="data_column" data_ref="input" numerical="True" use_header_names="true" label="Numerical column for x axis" />
+    <conditional name="cols">
+        <param name="header" type="select" label="Does the table have a header?" refresh_on_change="true" help="If the table has a header, the column can be selected using the name instead of the index.">
+            <option value="yes">yes</option>
+            <option value="no">no</option>
+        </param>
+        <when value="yes">
+          <param name="numerical_column" type="data_column" data_ref="input" numerical="True" use_header_names="true" label="Numerical column for x axis" />
+        </when>
+        <when value="no">
+          <param name="numerical_column" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" />
+        </when>
+    </conditional>
     <param name="breaks" type="integer" value="0" label="Number of breaks (bars)"/>
     <param name="title" type="text" value="Histogram" label="Plot title"/>
     <param name="xlab" type="text" value="V1" label="Label for x axis"/>