comparison omero_import.xml @ 3:83ccd2b525e5 draft

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

2:267227e757cb

<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@">1</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">omero</xref>
    </xrefs>
    <requirements>

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

        omero import folder -T Dataset:name:$dataset_name
            -s $omero_host
            -p $omero_port
            -u $__user__.extra_preferences.get('omero_account|username', $test_username)
            -w $__user__.extra_preferences.get('omero_account|password', $test_password)
        > $log &&

        omero logout
    ]]></command>
    <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>

3:83ccd2b525e5

<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>

            #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>