Mercurial > repos > goeckslab > rename_tiff_channels

diff rename_tiff_channels.xml @ 2:d2c59a1ac0c4 draft

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 130ef7e8ae6cab35866b72617e53d35acc11475a
author goeckslab
date Wed, 28 Feb 2024 20:52:08 +0000
parents 18f6be63414c
children 61fd94c7ce42
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--- a/rename_tiff_channels.xml	Wed Oct 05 20:39:20 2022 +0000
+++ b/rename_tiff_channels.xml	Wed Feb 28 20:52:08 2024 +0000
@@ -1,11 +1,14 @@
-<tool id="rename_tiff_channels" name="Rename OME-TIFF Channels" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
-    <description>Change the channel names in the XML metadata of OME-TIFF images</description>
+<tool id="rename_tiff_channels" name="Rename OME-TIFF channels" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>with ome-types</description>
     <macros>
         <import>macros.xml</import>
     </macros>
- 
+
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+
     <expand macro="requirements"/>
-    <expand macro="version_cmd"/>
 
     <stdio>
         <regex match=".*XMLSyntaxError.*"
@@ -14,6 +17,8 @@
                description="XML metadata does not adhere to OME format. Considering converting image to OME-TIFF" />
     </stdio>
 
+    <expand macro="version_cmd"/>
+
     <command detect_errors="aggressive"><![CDATA[
 
         cp '$image' ./renamed_image.ome.tiff && 
@@ -81,6 +86,9 @@
         </test>
     </tests>
     <help><![CDATA[
+    Given an OME.TIFF image and channel metadata CSV file, rename the image channels in the 
+    OME XML metadata. CSV file must contain column 'marker_name' which will populate the XML
+    metadata with channel names in the order provided in the CSV file. 
     ]]></help>
     <expand macro="citations" />
 </tool>