annotate omero_import.xml @ 3:83ccd2b525e5 draft

planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 266752b0162fbdb32f132a6702cb661ae36f48f0

<tool id="omero_import" name="OMERO Image Import" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
    <description> with omero-py </description>
    <macros>
        <token name="@TOOL_VERSION@">5.18.0</token>
        <token name="@VERSION_SUFFIX@">2</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">omero</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">omero-py</requirement>
        <!-- openjdk is needed: https://github.com/conda-forge/omero-py-feedstock/pull/16 -->
        <requirement type="package" version="21.0.2">openjdk</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #import re

        mkdir folder &&
        #for $image in $folder:
            #set image = $image
            #set image_identifier = re.sub('[^\s\w\-]', '_', str($image.element_identifier))
            ln -s '${image}' folder/'${image_identifier}.$image.ext' &&
        #end for

        source '$credentials' &&
        omero import folder -T Dataset:name:$dataset_name
            -s $omero_host
            -p $omero_port
            -u "\$OMERO_USER"
            -w "\$OMERO_PASSWORD"
        > $log &&

        omero logout
    ]]></command>
    <configfiles>
        <configfile name="credentials"><![CDATA[
export OMERO_USER="$__user__.extra_preferences.get('omero_account|username', $test_username)"
export OMERO_PASSWORD="$__user__.extra_preferences.get('omero_account|password', $test_password)"
        ]]></configfile>
    </configfiles>
    <inputs>
        <param name="folder" type="data" format="avi,bmp,btf,cif,csv,eps,fits,fli,gif,hdr,html,jp2,jpg,mov,mrc,ndpi,nhdr,nrrd,ome.tiff,par,pbm,pcx,pgm,png,ppm,psd,scn,sif,svs,tf2,tf8,tif,tif,tiff,top,txt,vms,wav,xml,zip" multiple="true" optional="false" label="Images to import into OMERO"/>
        <param name="dataset_name" type="text" optional="false" label="Target Dataset Name"/>
        <param name="omero_host" type="text" label="OMERO host URL">
            <validator type="regex" message="Enter a valid host location, for example, your.omero.server">^[a-zA-Z0-9._-]*$</validator>
            <validator type="expression" message="No two dots (..) allowed">'..' not in value</validator>
        </param>
        <param name="omero_port" type="integer" value="4064" optional="false" label="OMERO port"/>
        <param name="test_username" type="hidden" value=""/>
        <param name="test_password" type="hidden" value=""/>
    </inputs>
    <outputs>
        <data name="log" format="txt"/>
    </outputs>
    <tests>
        <test>
            <param name="folder" value="input1.tif,input2.tif"/>
            <param name="dataset_name" value="galaxy_test_upload"/>
            <param name="omero_host" value="host.docker.internal"/>
            <param name="omero_port" value="6064"/>
            <param name="test_username" value="root"/>
            <param name="test_password" value="omero"/>
            <output name="log" value="omero_output.txt" ftype="txt">
                <assert_contents>
                    <has_n_lines n="2"/>
                </assert_contents>
            </output>
            <assert_stderr>
                <has_text_matching expression="IMPORT_DONE.*input1.tif"/>
                <has_text_matching expression="IMPORT_DONE.*input2.tif"/>
                <has_text text="files uploaded, 2 filesets created, 2 images imported, 0 errors"/>
            </assert_stderr>
        </test>
    </tests>
    <help>
        - This tool allows the import of images into a user-defined OMERO server

        - The user can define an existing dataset name where the images will be imported

        - If the dataset does not exist, a new one will be created
    </help>
    <citations>
        <citation type="doi">10.1038/nmeth.1896</citation>
    </citations>
</tool>