comparison omero_import.xml @ 4:d0c0f3c95368 draft

planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2

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>
        <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:

            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>

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>

4:d0c0f3c95368

<tool id="omero_import" name="OMERO Image Import" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
    <description> with omero-py </description>
    <macros>
        <import>macros.xml</import>
        <token name="@VERSION_SUFFIX@">3</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">omero</xref>
    </xrefs>
    <expand macro="omeropy_requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        #import re

        mkdir folder &&
        #for $image in $folder:

            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"
        > $log &&

        omero logout
    ]]></command>
    <configfiles>

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>
        <expand macro="host_port"/>
        <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"/>
    </inputs>
    <outputs>
        <data name="log" format="txt"/>
    </outputs>
    <tests>