Mercurial > repos > goeckslab > rename_tiff_channels

changeset 2:d2c59a1ac0c4 draft default tip

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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 09e240a12897
children
files macros.xml rename_tiff_channels.xml
diffstat 2 files changed, 14 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Wed Oct 05 20:39:20 2022 +0000
+++ b/macros.xml	Wed Feb 28 20:52:08 2024 +0000
@@ -11,10 +11,11 @@
     </xml>
     <xml name="citations">
         <citations>
+        <citation type="doi">10.1101/2022.08.18.504436</citation>
         </citations>
     </xml>
 
     <token name="@TOOL_VERSION@">0.0.1</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">3</token>
     <token name="@PROFILE@">19.01</token>
 </macros>
--- 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>