# HG changeset patch
# User imgteam
# Date 1549739799 18000
# Node ID 784d5cf56c82c2e144bc57e5dd6c9371e2badfcc

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581

diff -r 000000000000 -r 784d5cf56c82 count_objects.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/count_objects.py	Sat Feb 09 14:16:39 2019 -0500
@@ -0,0 +1,21 @@
+#!/usr/bin/python
+
+import argparse
+import numpy as np
+import os
+import skimage.io
+from skimage.measure import regionprops
+
+parser = argparse.ArgumentParser(description='Count Objects')
+parser.add_argument('input_file', type=argparse.FileType('r'),
+                    help='Label input file')
+parser.add_argument('output_file', type=argparse.FileType('w'),
+                    help='Tabular output file')
+args = parser.parse_args()
+
+img_raw = skimage.io.imread(args.input_file.name)
+res = len(regionprops(img_raw))
+
+text_file = open(args.output_file.name, "w")
+text_file.write("objects\n%s" % res)
+text_file.close()
diff -r 000000000000 -r 784d5cf56c82 count_objects.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/count_objects.xml	Sat Feb 09 14:16:39 2019 -0500
@@ -0,0 +1,32 @@
+<tool id="ip_count_objects" name="Count Objects" version="0.0.4">
+    <description>in labled images</description>
+    <requirements>
+        <requirement type="package" version="0.14.2">scikit-image</requirement>
+        <requirement type="package" version="1.15.4">numpy</requirement>
+    </requirements>
+    <command>
+    <![CDATA[
+        python '$__tool_directory__/count_objects.py' '$input' '$output'
+    ]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="tiff" label="Source file" />
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="input.tiff"/>
+            <output name="output" value="table.tsv" ftype="tabular"/>
+        </test>
+    </tests>
+    <help>
+    **What it does**
+
+    This tool counts objects in a labeled image.
+    </help>
+    <citations>
+        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 784d5cf56c82 test-data/input.tiff
Binary file test-data/input.tiff has changed
diff -r 000000000000 -r 784d5cf56c82 test-data/table.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/table.tsv	Sat Feb 09 14:16:39 2019 -0500
@@ -0,0 +1,2 @@
+objects
+11
\ No newline at end of file