# HG changeset patch
# User thomaswollmann
# Date 1547670660 18000
# Node ID 832336936bc5a98e39cfb9851996134e79b8a014

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/count_objects/ commit d93e1dd276027cfc3fb518236110395a23d96f66

diff -r 000000000000 -r 832336936bc5 count_objects.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/count_objects.py	Wed Jan 16 15:31:00 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 832336936bc5 count_objects.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/count_objects.xml	Wed Jan 16 15:31:00 2019 -0500
@@ -0,0 +1,31 @@
+<?xml version="1.0"?>
+<tool name="Count Objects" id="ip_count_objects" version="0.0.4">
+  <description>Count Objects</description>
+  <requirements>
+    <requirement type="package" version="0.14.0">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.csv" ftype="tabular"/>
+    </test>
+  </tests>
+    <help>
+    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 832336936bc5 test-data/input.tiff
Binary file test-data/input.tiff has changed
diff -r 000000000000 -r 832336936bc5 test-data/table.csv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/table.csv	Wed Jan 16 15:31:00 2019 -0500
@@ -0,0 +1,2 @@
+objects
+11
\ No newline at end of file