| Previous changeset 1:09e240a12897 (2022-10-05) Next changeset 3:5cace2b0f933 (2024-05-10) |
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Commit message:
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 130ef7e8ae6cab35866b72617e53d35acc11475a |
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modified:
macros.xml rename_tiff_channels.xml |
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| diff -r 09e240a12897 -r d2c59a1ac0c4 macros.xml --- a/macros.xml Wed Oct 05 20:39:20 2022 +0000 +++ b/macros.xml Wed Feb 28 20:52:08 2024 +0000 |
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| @@ -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> |
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| diff -r 09e240a12897 -r d2c59a1ac0c4 rename_tiff_channels.xml --- 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 |
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| @@ -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> |