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changeset 0:8c25d4ff0b51 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/image_info/ commit 982cc5470b2032b5b85077500c17a020d0d25fd6
author imgteam
date Fri, 19 Jul 2019 07:29:08 -0400
parents
children 7b6d9412c7f8
files image_info.xml test-data/input.tiff test-data/res.txt
diffstat 3 files changed, 82 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/image_info.xml	Fri Jul 19 07:29:08 2019 -0400
@@ -0,0 +1,31 @@
+<tool id="ip_imageinfo" name="Image Info" version="0.1">
+  <description>Show Image Info</description>
+  <requirements>
+        <requirement type="package" version="5.7.1">bftools</requirement>
+  </requirements>
+  <command>
+        <![CDATA[
+        showinf '$input_file' -no-upgrade -minmax -nopix > '$output'
+        ]]>
+  </command>
+  <inputs>
+    <param label="Input Image" name="input_file" type="data" format="tiff,tif,png,jpeg,bmp"/>
+  </inputs>
+  <outputs>
+     <data format="txt" name="output"/>
+  </outputs>
+  <tests>
+        <test>
+            <param name="input_file" value="input.tiff" />
+            <output name="output" value="res.txt" ftype="txt" compare="diff" lines_diff="6"/>
+        </test>
+  </tests>    
+  <help>
+    **What it does**
+
+    Extracts metadata from an image.
+    </help>
+    <citations>
+        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
+    </citations>
+</tool>
Binary file test-data/input.tiff has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/res.txt	Fri Jul 19 07:29:08 2019 -0400
@@ -0,0 +1,51 @@
+Checking file format [Tagged Image File Format]
+Initializing reader
+TiffDelegateReader initializing input.tiff
+Reading IFDs
+Populating metadata
+Checking comment style
+Populating OME metadata
+Initialization took 0.068s
+
+Reading core metadata
+filename = input.tiff
+Series count = 1
+Series #0 :
+	Image count = 1
+	RGB = true (4) 
+	Interleaved = false
+	Indexed = false (false color)
+	Width = 265
+	Height = 530
+	SizeZ = 1
+	SizeT = 1
+	SizeC = 4 (effectively 1)
+	Thumbnail size = 64 x 128
+	Endianness = intel (little)
+	Dimension order = XYCZT (certain)
+	Pixel type = uint16
+	Valid bits per pixel = 16
+	Metadata complete = true
+	Thumbnail series = false
+	-----
+	Plane #0 <=> Z 0, C 0, T 0
+
+
+Reading global metadata
+BitsPerSample: 16
+Compression: Uncompressed
+DateTime: 2018:12:06 12:57:33
+ExtraSamples: 1
+ImageLength: 530
+ImageWidth: 265
+MetaDataPhotometricInterpretation: RGB
+MetaMorph: no
+NewSubfileType: 0
+NumberOfChannels: 4
+PhotometricInterpretation: RGB
+PlanarConfiguration: Chunky
+SampleFormat: unsigned integer
+SamplesPerPixel: 4
+Software: tifffile.py
+
+Reading metadata