--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/points2label.py	Sat Feb 09 14:44:10 2019 -0500
@@ -0,0 +1,44 @@
+import argparse
+import sys
+import numpy as np
+import skimage.io
+import pandas as pd
+import warnings
+
+def points2label(labels, shape, output_file=None, has_header=False, is_TSV=True):
+    labelimg = np.zeros([shape[0], shape[1]], dtype=np.int32)
+
+    if is_TSV:
+        if has_header:
+            df = pd.read_csv(labels, sep='\t', skiprows=1, header=None)
+        else:
+            df = pd.read_csv(labels, sep='\t', header=None)
+    else:
+        if has_header:
+            df = pd.read_csv(labels, skiprows=1, header=None)
+        else:
+            df = pd.read_csv(labels, header=None)
+
+    for i in range(0, len(df)):
+        a_row = df.iloc[i]
+        labelimg[a_row[0], a_row[1]] = i+1
+
+    if output_file is not None:
+        with warnings.catch_warnings():
+            warnings.simplefilter("ignore")
+            skimage.io.imsave(output_file, labelimg, plugin='tifffile')
+    else:
+        return labelimg
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('label_file', type=argparse.FileType('r'), default=sys.stdin, help='label file')
+    parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file')
+    parser.add_argument('org_file', type=argparse.FileType('r'), default=sys.stdin, help='input original file')
+    parser.add_argument('--has_header', dest='has_header', type=bool, default=False, help='label file has header')
+    parser.add_argument('--is_tsv', dest='is_tsv', type=bool, default=True, help='label file is TSV')
+    args = parser.parse_args()
+
+    original_shape = skimage.io.imread(args.org_file.name, plugin='tifffile').shape
+
+    points2label(args.label_file.name, original_shape, args.out_file.name, args.has_header, args.is_tsv)

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/points2label.xml	Sat Feb 09 14:44:10 2019 -0500
@@ -0,0 +1,36 @@
+<tool id="ip_points_to_labe" name="Points to Label" version="0.2">
+    <description>Points to Label Image</description>
+    <requirements>
+        <requirement type="package" version="1.15.4">numpy</requirement>
+        <requirement type="package" version="0.14.2">scikit-image</requirement>
+        <requirement type="package" version="0.23.4">pandas</requirement>
+    </requirements>
+    <command>
+    <![CDATA[
+        python '$__tool_directory__/points2label.py' '$input' '$output' '$org_file' $has_header
+    ]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="tabular" label="Point CSV file"/>
+        <param name="org_file" type="data" format="tiff" label="Original label image file"/>
+        <param name="has_header" type="boolean" checked="false" truevalue="--has_header True" falsevalue="" optional="true" label="Does point file contain header?" /> 
+    </inputs>
+    <outputs>
+        <data name="output" format="tiff"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="points.tsv"/>
+            <param name="org_file" value="galaxyIcon_noText.tif"/>
+            <output name="output" file="out.tif" ftype="tiff" compare="sim_size"/>
+        </test>
+    </tests>
+    <help>
+    **What it does**
+
+    This tool converts points to a label image.
+    </help>
+    <citations>
+        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> 
+    </citations>
+</tool>

Binary file test-data/galaxyIcon_noText.tif has changed

Binary file test-data/out.tif has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/points.tsv	Sat Feb 09 14:44:10 2019 -0500
@@ -0,0 +1,7 @@
+5	3
+10	2
+8	4
+15	15
+8	5
+8	6
+8	7