comparison rename_tiff_channels.xml @ 2:d2c59a1ac0c4 draft

planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 130ef7e8ae6cab35866b72617e53d35acc11475a

1:09e240a12897

<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>
    <macros>
        <import>macros.xml</import>
    </macros>
 
    <expand macro="requirements"/>
    <expand macro="version_cmd"/>

    <stdio>
        <regex match=".*XMLSyntaxError.*"
               source="stderr"
               level="fatal"
               description="XML metadata does not adhere to OME format. Considering converting image to OME-TIFF" />
    </stdio>

    <command detect_errors="aggressive"><![CDATA[

        cp '$image' ./renamed_image.ome.tiff && 

                <has_text text="Updated OME-TIFF metadata" />
            </assert_stdout>
        </test>
    </tests>
    <help><![CDATA[
    ]]></help>
    <expand macro="citations" />
</tool>

2:d2c59a1ac0c4

<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"/>

    <stdio>
        <regex match=".*XMLSyntaxError.*"
               source="stderr"
               level="fatal"
               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 && 

                <has_text text="Updated OME-TIFF metadata" />
            </assert_stdout>
        </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>