annotate omero_filter.xml @ 1:375281d11535 draft

planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit d69e684236ce5d36a09e84f1eae6d8c98ed7499b

<tool id="omero_filter" name="OMERO IDs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
    <description> with ezomero </description>
    <macros>
        <import>macros.xml</import>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">omero</xref>
    </xrefs>
    <expand macro="ezomero_requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__'/omero_filter.py
        --credential-file '$credentials'
        @HOST_PORT@
        --filter $filter
        --value1 '$value1'
        --id $did
        --tsv_file '$tsv'
        #if $filter == "KP"
        --value2 '$value2'
        #end if

    ]]></command>
    <configfiles>
        <expand macro="credentials"/>
    </configfiles>
    <inputs>
        <expand macro="host_port"/>
        <conditional name = "filter_type">
            <param name="filter" type="select" optional="false" label="Filter type to apply:">
                <option value="filename">Filename</option>
                <option value="KP">Key-Value</option>
                <option value="tag">Tag</option>
            </param>
            <when value="filename">
                <param name="value1" type="text" label="Filename to search among the image IDs">
                    <validator type="regex" message="Enter a valid filename to search in the OMERO server">^[\w\-. ]+$</validator>
                </param>
                <param name="value2"  value="" type="hidden" label="Not necessary filter"/>
                <param name="did" type="text" label="List of images IDs">
                    <validator type="regex" message="Enter a valid list of IDs (i.e. 2,45,56,67)">^\d+(,\d+)*$</validator>
                </param>
            </when>
            <when value="KP">
                <param name="value1" type="text" label="Key Value to search among the image IDs">
                    <validator type="regex" message="Enter a valid Key to search in the OMERO server">^[\w\-. ]+$</validator>
                </param>
                <param name="value2" type="hidden" label="Pair Values to search among images IDs"/>
                <param name="did" type="text" label="List of images IDs">
                    <validator type="regex" message="Enter a valid list of IDs (i.e. 2,45,56,67)">^\d+(,\d+)*$</validator>
                </param>
            </when>
            <when value="tag">
                <param name="value1" type="text" label="Tag to search among the images IDs">
                    <validator type="regex" message="Enter a valid Key to search in the OMERO server">^[\w\-. ]+$</validator>
                </param>
                <param name="value2"  value="" optional="true" type="hidden" label="Not necessary filter"/>
                <param name="did" type="text" label="List of images IDs">
                    <validator type="regex" message="Enter a valid list of IDs (i.e. 2,45,56,67)">^(\d+)(,\d+)*$</validator>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="tsv" format="tabular"/>
    </outputs>
    <tests>
        <test>
            <param name="omero_host" value="host.docker.internal"/>
            <param name="omero_port" value="6064"/>
            <conditional name="filter_type">
                <param name="filter" value="filename"/>
                <param name="value1" value="sample_image_2.jpg"/>
                <param name="did" value="1,2"/>
            </conditional>
            <param name="test_username" value="root"/>
            <param name="test_password" value="omero"/>
            <output name="tsv" value="output_filter_filename.tsv" ftype="tabular">
                <assert_contents>
                    <has_text text="2"/>
                    <has_n_columns n="1"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="omero_host" value="host.docker.internal"/>
            <param name="omero_port" value="6064"/>
            <conditional name="filter_type">
                <param name="filter" value="tag"/>
                <param name="value1" value="test_tag"/>
                <param name="did" value="1,2"/>
            </conditional>
            <param name="test_username" value="root"/>
            <param name="test_password" value="omero"/>
            <output name="tsv" value="output_filter_tag.tsv" ftype="tabular">
                <assert_contents>
                    <has_text text="1"/>
                    <has_n_columns n="1"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
Description
-----------

- Tool to filter images IDs by filename, Key-Value Pairs and Tag value.
- For Key-Value Pairs search, two values are required (Value1 = Key, Value2 = Pair).
- IDs are a list of image IDs which can be fetched using the omero_get tool.

@SECURITY_DISCLAIMER@

    </help>
    <citations>
        <citation type="doi">10.1038/nmeth.1896</citation>
    </citations>
</tool>