# HG changeset patch
# User imgteam
# Date 1553097967 14400
# Node ID 5a210baa2ff15fb9c6a7f4deaa8a63524eee2e1a

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit 67eaf2b9a9ee1bfed14afba33007ef595890400c

diff -r 000000000000 -r 5a210baa2ff1 imagecoordinates_flipaxis.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imagecoordinates_flipaxis.py	Wed Mar 20 12:06:07 2019 -0400
@@ -0,0 +1,23 @@
+import argparse
+import pandas as pd
+
+
+def imagecoordinates_flipyaxis(input_file, output_file, image_height):
+    df = pd.read_csv(input_file, sep='\t')
+
+    x = df.copy().y # create copy instead of view
+    df.y = image_height-(df.x + 1) # since maximal y index = height-1 
+    df.x = x
+    df.to_csv(output_file, sep="\t", index=False)
+
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('input_file', type=argparse.FileType('r'), help='original file')
+    parser.add_argument('out_file_str', type=str, help='string of output file name')
+    # parser.add_argument('image_height', help='height of image')
+    parser.add_argument('image_height', type=int, help='height of image')
+    args = parser.parse_args()
+    imagecoordinates_flipyaxis(args.input_file.name, args.out_file_str, args.image_height)
+    # imagecoordinates_flipyaxis(args.input_file.name, args.out_file_str, int(args.image_height))
diff -r 000000000000 -r 5a210baa2ff1 imagecoordinates_flipaxis.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imagecoordinates_flipaxis.xml	Wed Mar 20 12:06:07 2019 -0400
@@ -0,0 +1,30 @@
+<tool id="imagecoordinates_flipaxis" name="Switch axis coordinates" version="0.1"> 
+  <description>Switches the axes of an image and flips the y axis.</description>
+  <requirements> 
+    <requirement type="package" version="0.23.4" >pandas</requirement>
+  </requirements>
+  <command detect_errors="aggressive"> 
+        <![CDATA[
+        python "$__tool_directory__/imagecoordinates_flipaxis.py" '$input' '$output' $img_height
+        ]]> 
+  </command>
+  <inputs> 
+    <param name="input" type="data" format="tabular" label="File with image coordinates"/> 
+    <param name="img_height" type="integer" value="100" label="Height of the corresponding image"/>
+  </inputs>
+  <outputs>
+    <data name="output" format="tabular"/>
+  </outputs>
+  <tests>
+    <test>
+	    <param name="input" value="table.tsv" />
+      <param name="img_height" value="500"/>
+      <output name="output" value="out2.tsv" ftype="tabular" />
+    </test>
+  </tests>
+  <help>Makes x the horizontal axis (left to right) and y the vertical axis (bottom to top), 
+  like in a coordinate system.</help>
+  <citations>
+      <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
+  </citations>
+</tool>
diff -r 000000000000 -r 5a210baa2ff1 test-data/out2.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out2.tsv	Wed Mar 20 12:06:07 2019 -0400
@@ -0,0 +1,7 @@
+x	y
+4	495
+104	494
+204	493
+34	492
+4	491
+4	490
diff -r 000000000000 -r 5a210baa2ff1 test-data/table.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/table.tsv	Wed Mar 20 12:06:07 2019 -0400
@@ -0,0 +1,7 @@
+x	y
+4	4
+5	104
+6	204
+7	34
+8	4
+9	4