From ecfbb3bc347fbc313f04ec35495b27d01bbac882 Mon Sep 17 00:00:00 2001
From: Helge Hecht <helge.hecht@recetox.muni.cz>
Date: Mon, 3 Feb 2025 10:55:52 +0000
Subject: [PATCH 01/10] Update scatterplot.xml to use header names

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

diff --git a/tools/scatterplot/scatterplot.xml b/tools/scatterplot/scatterplot.xml
index 29b841f8..0983f81f 100644
--- a/tools/scatterplot/scatterplot.xml
+++ b/tools/scatterplot/scatterplot.xml
@@ -17,8 +17,8 @@
   </command>
   <inputs>
     <param name="input" type="data" format="tabular" label="Dataset" help="Dataset missing? See TIP below"/>
-    <param name="col1" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" />
-    <param name="col2" type="data_column" data_ref="input" numerical="True" label="Numerical column for y axis" />
+    <param name="col1" type="data_column" data_ref="input" use_header_names="true" numerical="True" label="Numerical column for x axis" />
+    <param name="col2" type="data_column" data_ref="input" use_header_names="true" numerical="True" label="Numerical column for y axis" />
     <param name="title" type="text" value="Scatterplot" label="Plot title"/>
     <param name="xlab" type="text" value="V1" label="Label for x axis"/>
     <param name="ylab" type="text" value="V2" label="Label for y axis"/>

From df2fbf509d90cf6c6effc8ff2a056dbc99d90749 Mon Sep 17 00:00:00 2001
From: Helge Hecht <helge.hecht@recetox.muni.cz>
Date: Mon, 3 Feb 2025 10:56:58 +0000
Subject: [PATCH 02/10] Update scatterplot.xml

---
 tools/scatterplot/scatterplot.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/scatterplot/scatterplot.xml b/tools/scatterplot/scatterplot.xml
index 0983f81f..d6c7904a 100644
--- a/tools/scatterplot/scatterplot.xml
+++ b/tools/scatterplot/scatterplot.xml
@@ -1,4 +1,4 @@
-<tool id="scatterplot_rpy" name="Scatterplot" version="1.0.3">
+<tool id="scatterplot_rpy" name="Scatterplot" version="1.0.3+galaxy0">
   <description>of two numeric columns</description>
   <requirements>
     <requirement type="package" version="1.9">numpy</requirement>

From a7015f788e5339fc6d72a47a74461025227b0aa3 Mon Sep 17 00:00:00 2001
From: hechth <helge.hecht@recetox.muni.cz>
Date: Mon, 3 Feb 2025 13:35:44 +0100
Subject: [PATCH 03/10] fixed linting

---
 tools/scatterplot/.shed.yml       | 1 +
 tools/scatterplot/scatterplot.xml | 1 +
 2 files changed, 2 insertions(+)

diff --git a/tools/scatterplot/.shed.yml b/tools/scatterplot/.shed.yml
index cf028276..7fe3d832 100644
--- a/tools/scatterplot/.shed.yml
+++ b/tools/scatterplot/.shed.yml
@@ -8,4 +8,5 @@ long_description: |
 name: scatterplot
 owner: devteam
 remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot
+homepage_url: https://github.com/galaxyproject/tools-devteam/
 type: unrestricted
diff --git a/tools/scatterplot/scatterplot.xml b/tools/scatterplot/scatterplot.xml
index d6c7904a..e824b769 100644
--- a/tools/scatterplot/scatterplot.xml
+++ b/tools/scatterplot/scatterplot.xml
@@ -76,5 +76,6 @@ This tool creates a simple scatter plot between two variables containing numeric
 ]]>
 </help>
 <citations>
+  <citation type="doi">10.1038/s41586-020-2649-2</citation>
 </citations>
 </tool>

From 2b79bf913ab93420e90ae5ae59e773344298a08e Mon Sep 17 00:00:00 2001
From: hechth <helge.hecht@recetox.muni.cz>
Date: Mon, 3 Feb 2025 13:40:58 +0100
Subject: [PATCH 04/10] linted python script

---
 tools/scatterplot/scatterplot.py | 51 +++++++++++++++++++-------------
 1 file changed, 30 insertions(+), 21 deletions(-)

diff --git a/tools/scatterplot/scatterplot.py b/tools/scatterplot/scatterplot.py
index c9ffad9e..55bec8c8 100644
--- a/tools/scatterplot/scatterplot.py
+++ b/tools/scatterplot/scatterplot.py
@@ -24,9 +24,11 @@ def main():
     in_fname = sys.argv[1]
     out_fname = sys.argv[2]
     try:
-        columns = int( sys.argv[3] ) - 1, int( sys.argv[4] ) - 1
-    except:
-        stop_err( "Columns not specified, your query does not contain a column of numerical data." )
+        columns = int(sys.argv[3]) - 1, int(sys.argv[4]) - 1
+    except Exception:
+        stop_err(
+            "Columns not specified, your query does not contain a column of numerical data."
+        )
     title = sys.argv[5]
     xlab = sys.argv[6]
     ylab = sys.argv[7]
@@ -34,31 +36,31 @@ def main():
     matrix = []
     skipped_lines = 0
     first_invalid_line = 0
-    invalid_value = ''
+    invalid_value = ""
     invalid_column = 0
     i = 0
-    for i, line in enumerate( open( in_fname ) ):
+    for i, line in enumerate(open(in_fname)):
         valid = True
-        line = line.rstrip( '\r\n' )
-        if line and not line.startswith( '#' ):
+        line = line.rstrip("\r\n")
+        if line and not line.startswith("#"):
             row = []
-            fields = line.split( "\t" )
+            fields = line.split("\t")
             for column in columns:
                 try:
                     val = fields[column]
                     if val.lower() == "na":
-                        row.append( float( "nan" ) )
+                        row.append(float("nan"))
                     else:
-                        row.append( float( fields[column] ) )
-                except:
+                        row.append(float(fields[column]))
+                except Exception:
                     valid = False
                     skipped_lines += 1
                     if not first_invalid_line:
                         first_invalid_line = i + 1
                         try:
                             invalid_value = fields[column]
-                        except:
-                            invalid_value = ''
+                        except Exception:
+                            invalid_value = ""
                         invalid_column = column + 1
                     break
         else:
@@ -68,22 +70,29 @@ def main():
                 first_invalid_line = i + 1
 
         if valid:
-            matrix.append( row )
+            matrix.append(row)
 
     if skipped_lines < i:
         try:
-            a = numpy2ri(array( matrix ))
-            r.pdf( out_fname, 8, 8 )
-            r.plot( a, type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19 )
+            a = numpy2ri(array(matrix))
+            r.pdf(out_fname, 8, 8)
+            r.plot(a, type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19)
             r.dev_off()
         except Exception as exc:
-            stop_err( "%s" % str( exc ) )
+            stop_err("%s" % str(exc))
     else:
-        stop_err( "All values in both columns %s and %s are non-numeric or empty." % ( sys.argv[3], sys.argv[4] ) )
+        stop_err(
+            "All values in both columns %s and %s are non-numeric or empty."
+            % (sys.argv[3], sys.argv[4])
+        )
 
-    print("Scatter plot on columns %s, %s. " % ( sys.argv[3], sys.argv[4] ))
+    print("Scatter plot on columns %s, %s. " % (sys.argv[3], sys.argv[4]))
     if skipped_lines > 0:
-        print("Skipped %d lines starting with line #%d, value '%s' in column %d is not numeric." % ( skipped_lines, first_invalid_line, invalid_value, invalid_column ))
+        print(
+            "Skipped %d lines starting with line #%d, value '%s' in column %d is not numeric."
+            % (skipped_lines, first_invalid_line, invalid_value, invalid_column)
+        )
+
 
 if __name__ == "__main__":
     main()

From dce77d4ea50493c8d1ad5a878081089776f2066d Mon Sep 17 00:00:00 2001
From: hechth <helge.hecht@recetox.muni.cz>
Date: Mon, 3 Feb 2025 13:44:01 +0100
Subject: [PATCH 05/10] lint

---
 tools/scatterplot/scatterplot.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/scatterplot/scatterplot.py b/tools/scatterplot/scatterplot.py
index 55bec8c8..eb6905a2 100644
--- a/tools/scatterplot/scatterplot.py
+++ b/tools/scatterplot/scatterplot.py
@@ -5,8 +5,8 @@
 
 import sys
 
-from numpy import array
 import rpy2.rpy_classic as rpy
+from numpy import array
 from rpy2.robjects.numpy2ri import numpy2ri
 
 

From 7e7e6625b5fa1c5221b774a794bfe3e73f3a3022 Mon Sep 17 00:00:00 2001
From: hechth <helge.hecht@recetox.muni.cz>
Date: Mon, 3 Feb 2025 14:32:02 +0100
Subject: [PATCH 06/10] added missing dependency

---
 tools/scatterplot/scatterplot.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tools/scatterplot/scatterplot.xml b/tools/scatterplot/scatterplot.xml
index e824b769..3fe990ed 100644
--- a/tools/scatterplot/scatterplot.xml
+++ b/tools/scatterplot/scatterplot.xml
@@ -3,6 +3,7 @@
   <requirements>
     <requirement type="package" version="1.9">numpy</requirement>
     <requirement type="package" version="2.8.5">rpy2</requirement>
+    <requirement type="package" version="3.0">libgfortran</requirement>
   </requirements>
   <command><![CDATA[
       python '$__tool_directory__/scatterplot.py'

From 8189ba4482939044172f9872bb82df83d5ae199c Mon Sep 17 00:00:00 2001
From: hechth <helge.hecht@recetox.muni.cz>
Date: Tue, 4 Feb 2025 10:58:30 +0100
Subject: [PATCH 07/10] fixed bug introduced through changing import order

---
 tools/scatterplot/scatterplot.py  |  2 +-
 tools/scatterplot/scatterplot.xml | 22 ++++++++++++++++++++--
 2 files changed, 21 insertions(+), 3 deletions(-)

diff --git a/tools/scatterplot/scatterplot.py b/tools/scatterplot/scatterplot.py
index eb6905a2..55bec8c8 100644
--- a/tools/scatterplot/scatterplot.py
+++ b/tools/scatterplot/scatterplot.py
@@ -5,8 +5,8 @@
 
 import sys
 
-import rpy2.rpy_classic as rpy
 from numpy import array
+import rpy2.rpy_classic as rpy
 from rpy2.robjects.numpy2ri import numpy2ri
 
 
diff --git a/tools/scatterplot/scatterplot.xml b/tools/scatterplot/scatterplot.xml
index 3fe990ed..96257194 100644
--- a/tools/scatterplot/scatterplot.xml
+++ b/tools/scatterplot/scatterplot.xml
@@ -5,6 +5,11 @@
     <requirement type="package" version="2.8.5">rpy2</requirement>
     <requirement type="package" version="3.0">libgfortran</requirement>
   </requirements>
+<!-- 
+  <environment_variables>
+    <environment_variable name="R_HOME">\$(R RHOME)</environment_variable>
+  </environment_variables> -->
+
   <command><![CDATA[
       python '$__tool_directory__/scatterplot.py'
         '$input'
@@ -18,8 +23,21 @@
   </command>
   <inputs>
     <param name="input" type="data" format="tabular" label="Dataset" help="Dataset missing? See TIP below"/>
-    <param name="col1" type="data_column" data_ref="input" use_header_names="true" numerical="True" label="Numerical column for x axis" />
-    <param name="col2" type="data_column" data_ref="input" use_header_names="true" numerical="True" label="Numerical column for y 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, columns can be selected by name instead of the index.">
+            <option value="yes" selected="true">yes</option>
+            <option value="no">no</option>
+        </param>
+        <when value="yes">
+          <param name="col1" type="data_column" data_ref="input" use_header_names="true" numerical="True" label="Numerical column for x axis" />
+          <param name="col2" type="data_column" data_ref="input" use_header_names="true" numerical="True" label="Numerical column for y axis" />            
+        </when>
+        <when value="no">
+          <param name="col1" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" />
+          <param name="col2" type="data_column" data_ref="input" numerical="True" label="Numerical column for y axis" />
+        </when>
+    </conditional>
+
     <param name="title" type="text" value="Scatterplot" label="Plot title"/>
     <param name="xlab" type="text" value="V1" label="Label for x axis"/>
     <param name="ylab" type="text" value="V2" label="Label for y axis"/>

From d372edf16a176591e6b822a7e0cbb792e58276e4 Mon Sep 17 00:00:00 2001
From: hechth <helge.hecht@recetox.muni.cz>
Date: Tue, 4 Feb 2025 12:56:30 +0100
Subject: [PATCH 08/10] skip linting for this

---
 tools/scatterplot/scatterplot.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tools/scatterplot/scatterplot.py b/tools/scatterplot/scatterplot.py
index 55bec8c8..07882ebd 100644
--- a/tools/scatterplot/scatterplot.py
+++ b/tools/scatterplot/scatterplot.py
@@ -1,6 +1,8 @@
 #!/usr/bin/env python
 # Greg Von Kuster
 
+# pylint: skip-file
+
 from __future__ import print_function
 
 import sys

From 91ca2de56b185d14edaa992045c5e15c08566cab Mon Sep 17 00:00:00 2001
From: hechth <helge.hecht@recetox.muni.cz>
Date: Tue, 4 Feb 2025 13:05:39 +0100
Subject: [PATCH 09/10] ignore import error, hopefully

---
 tools/scatterplot/scatterplot.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/scatterplot/scatterplot.py b/tools/scatterplot/scatterplot.py
index 07882ebd..fa11f7e3 100644
--- a/tools/scatterplot/scatterplot.py
+++ b/tools/scatterplot/scatterplot.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # Greg Von Kuster
 
-# pylint: skip-file
+# noqa: I100
 
 from __future__ import print_function
 

From 3bae6a71438bcafed0e7ba36e695ee080c5bcfca Mon Sep 17 00:00:00 2001
From: hechth <helge.hecht@recetox.muni.cz>
Date: Tue, 4 Feb 2025 13:27:57 +0100
Subject: [PATCH 10/10] ignore lint next attempt

---
 tools/scatterplot/scatterplot.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/scatterplot/scatterplot.py b/tools/scatterplot/scatterplot.py
index fa11f7e3..17fa9035 100644
--- a/tools/scatterplot/scatterplot.py
+++ b/tools/scatterplot/scatterplot.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # Greg Von Kuster
 
-# noqa: I100
+# flake8: noqa
 
 from __future__ import print_function