Mercurial > repos > watsocam > rename_tiff_channels

changeset 3:b18d4cf55493 draft default tip

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils/rename_tiff_channels commit c631fe8ad37829090b815fc911a10150cd39cd42
author goeckslab
date Tue, 12 Jul 2022 20:55:09 +0000
parents 75f8fcef3e96
children
files rename_tiff_channels.py rename_tiff_channels.xml
diffstat 2 files changed, 10 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/rename_tiff_channels.py	Wed May 11 19:32:51 2022 +0000
+++ b/rename_tiff_channels.py	Tue Jul 12 20:55:09 2022 +0000
@@ -1,9 +1,9 @@
-import sys
-import pandas
+import bioformats
 import click
+import javabridge
+import pandas
 import tifffile
-import bioformats
-import javabridge
+
 
 @click.command()
 @click.argument('input_tiff', type=str)
@@ -38,7 +38,7 @@
     removed_ome = '<'.join(xml_str.split('<ome:'))
     removed_ome = '/'.join(removed_ome.split('/ome:'))
     with open(output_name, "w") as out_tiff:
-        out_tiff.write(header+removed_ome)
+        out_tiff.write(header + removed_ome)
 
     # Slay the evil JavaBridge
     javabridge.kill_vm()
--- a/rename_tiff_channels.xml	Wed May 11 19:32:51 2022 +0000
+++ b/rename_tiff_channels.xml	Tue Jul 12 20:55:09 2022 +0000
@@ -1,16 +1,16 @@
-<tool id="rename_tiff_channels" name="Rename OME-TIFF Channels" version="@VERSION@.2" profile="17.09">
+<tool id="rename_tiff_channels" name="Rename OME-TIFF Channels" version="@VERSION@.2" profile="19.01">
     <description>A simple script to change the channel names in the XML metadata of OME-TIFF images</description>
     <macros>
         <import>macros.xml</import>
     </macros>
  
     <expand macro="requirements"/>
-    @VERSION_CMD@
+    <expand macro="version_cmd"/>
 
     <command detect_errors="exit_code"><![CDATA[
-        cp "$image" "$renamed_image" ; 
-        @CMD_BEGIN@ "$image" "$channel_csv" out.xml ;
-        tiffcomment -set out.xml "$renamed_image" ;
+        cp '$image' '$renamed_image' && 
+        @CMD_BEGIN@ '$image' '$channel_csv' out.xml &&
+        tiffcomment -set out.xml '$renamed_image'
     ]]></command>
 
     <inputs>