Mercurial > repos > goeckslab > rename_tiff_channels

comparison rename_tiff_channels.xml @ 2:d2c59a1ac0c4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
comparison
equal deleted inserted replaced
1:09e240a12897 2:d2c59a1ac0c4
1 <tool id="rename_tiff_channels" name="Rename OME-TIFF Channels" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="rename_tiff_channels" name="Rename OME-TIFF channels" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Change the channel names in the XML metadata of OME-TIFF images</description> 2 <description>with ome-types</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 6
7 <edam_operations>
8 <edam_operation>operation_3443</edam_operation>
9 </edam_operations>
10
7 <expand macro="requirements"/> 11 <expand macro="requirements"/>
8 <expand macro="version_cmd"/>
9 12
10 <stdio> 13 <stdio>
11 <regex match=".*XMLSyntaxError.*" 14 <regex match=".*XMLSyntaxError.*"
12 source="stderr" 15 source="stderr"
13 level="fatal" 16 level="fatal"
14 description="XML metadata does not adhere to OME format. Considering converting image to OME-TIFF" /> 17 description="XML metadata does not adhere to OME format. Considering converting image to OME-TIFF" />
15 </stdio> 18 </stdio>
19
20 <expand macro="version_cmd"/>
16 21
17 <command detect_errors="aggressive"><![CDATA[ 22 <command detect_errors="aggressive"><![CDATA[
18 23
19 cp '$image' ./renamed_image.ome.tiff && 24 cp '$image' ./renamed_image.ome.tiff &&
20 25
79 <has_text text="Updated OME-TIFF metadata" /> 84 <has_text text="Updated OME-TIFF metadata" />
80 </assert_stdout> 85 </assert_stdout>
81 </test> 86 </test>
82 </tests> 87 </tests>
83 <help><![CDATA[ 88 <help><![CDATA[
89 Given an OME.TIFF image and channel metadata CSV file, rename the image channels in the
90 OME XML metadata. CSV file must contain column 'marker_name' which will populate the XML
91 metadata with channel names in the order provided in the CSV file.
84 ]]></help> 92 ]]></help>
85 <expand macro="citations" /> 93 <expand macro="citations" />
86 </tool> 94 </tool>