comparison idr_download_by_ids.xml @ 13:f92941d1a85e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f

12:4b794652dcdc

<?xml version="1.0"?>
<tool id="idr_download_by_ids" name="Download IDR/OMERO" version="0.44.1" profile="18.09">
    <description></description>
    <macros>
        <xml name="region_spec" token_pos="upper-left corner">
            <param name="x_coord" type="integer" value="0" min="0"
            label="x-coordinate of region @POS@" />

    </macros>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <requirements>
        <requirement type="package" version="5.10.1">omero-py</requirement>
        <requirement type="package" version="0.4.2">pylibtiff</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        
        #if $omero_instance_type.omero_instance == "priv":
            ## the user wants to use a non-public OMERO instance

        #if str($image_ids.source) == 'omeroDatasetID':
            --dataset
        #end if
        #if $image_region.original == "original":
            --download-original
        #else:
            #set $channel = str($image_region.channel).strip()
            #if $channel:
                -c '$channel'
            #end if

    "username": "$username",
    "password": "$password"
}
        ]]></configfile>
    </configfiles>
<inputs>
        <conditional name="omero_instance_type">
            <param name="omero_instance" type="select" label="Which OMERO instance to connect?"
                   help="By default, the tool will download a tarball containing individual images from IDR into your Galaxy history. If you 
                   need to connect to your own instance, set your connection username and password from User->Preference->Manage Information" >
                <option value="idr">IDR</option>

        </conditional>

        <conditional name="image_region">
            <param name="original" type="select" label="Which images do you want to download?">
                <option value="TIFF" selected="true">Exported TIFF (single channel, single stack)</option>
                <option value="original">Original file (file uploaded to omero, only available for private instances)</option>
            </param>
            <when value="original"/>
            <when value="TIFF">
                <param name="channel" type="text"
                    label="Name of the channel to download"
                    help="For all image IDs only the specified channel will be downloaded. If left empty, the first channel (whatever this is) will be downloaded by default." />
                <param name="z_section" type="integer" value="0" min="0"

        <data name="output_tar" format="tar" from_work_dir="./downloads/images.tar" label ="Images tarball">
            <filter>download_tar</filter>
        </data> 
    </outputs>
    <tests>
        <test>
            <conditional name="omero_instance_type">
                 <param name="omero_instance" value="idr" />
            </conditional>
            <param name="source" value="dataset" />
            <param name="id_spec" value="ids.txt" />

                </conditional>
                <param name="frame" value="0" />
            </conditional>
            <param name="download_tar" value="false" />
            <output_collection name="output_file" type="list">
                <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test0.tiff"/>
            </output_collection>
        </test>
        <test>
            <conditional name="omero_instance_type">
                 <param name="omero_instance" value="idr" />
            </conditional>
            <param name="source" value="link" />
            <param name="id_spec" value="1884807" />

                </conditional>
                <param name="frame" value="2" />
            </conditional>
            <param name="download_tar" value="false" />
            <output_collection name="output_file" type="list">
                <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test1.tiff"/>
            </output_collection>
        </test>
        <test>
            <conditional name="omero_instance_type">
                 <param name="omero_instance" value="idr" />
            </conditional>
            <param name="source" value="link" />
            <param name="id_spec" value="1884807" />

                </conditional>
                <param name="frame" value="2" />
            </conditional>
            <param name="download_tar" value="false" />
            <output_collection name="output_file" type="list">
                <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test2.tiff"/>
            </output_collection>
        </test>
        <test>
            <conditional name="omero_instance_type">
                 <param name="omero_instance" value="idr" />
            </conditional>
            <param name="source" value="link" />
            <param name="id_spec" value="https://idr.openmicroscopy.org/webclient/?show=image-9036708|image-9036710|image-9036711" />

            </conditional>
            <param name="download_tar" value="false" />
            <output_collection name="output_file" type="list" count="3">
                <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024">
                    <assert_contents>
                        <has_size value="2097286" />
                    </assert_contents>
                </element>
            </output_collection>
            <output name="out_log">
                <assert_contents>

                </conditional>
                <param name="frame" value="20" />
            </conditional>
            <param name="download_tar" value="false" />
        </test>
        <test>
            <!-- Repeat test with non-existing image-ID 9036708999,
            but use skip-failed option -->
            <conditional name="omero_instance_type">
                 <param name="omero_instance" value="idr" />
            </conditional>

            <param name="skip_failed" value="true" />
            <param name="download_tar" value="false" />
            <output_collection name="output_file" type="list" count="2">
                <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024">
                    <assert_contents>
                        <has_size value="2097286" />
                    </assert_contents>
                </element>
            </output_collection>
            <output name="out_log">
                <assert_contents>

                    <has_text text="(ID: 9036710): Specified image plane (4) is out of bounds" />
                    <has_n_lines n="2"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <conditional name="omero_instance_type">
                 <param name="omero_instance" value="idr" />
            </conditional>
            <!-- Test for download images in a tarball -->
            <param name="source" value="dataset" />

                </conditional>
                <param name="frame" value="0" />
            </conditional>
            <output name="output_tar">
                    <assert_contents>
                        <has_size value="1382400" />
                        <has_archive_member path=".*/*__1828167__0__0__671__511.tiff" >
                            <has_size value="685896" />
                        </has_archive_member>
                        <has_archive_member path=".*/*__1828658__0__0__671__511.tiff" >
                            <has_size value="685896" />
                        </has_archive_member>
                    </assert_contents>
            </output>
        </test>
        <test>
            <conditional name="omero_instance_type">
                 <param name="omero_instance" value="priv" />
                 <param name="omero_host" value="idr.openmicroscopy.org" />
                 <param name="omero_secured" value="true" />
                 <param name="galaxy_test_param" value="true" />

                </conditional>
                <param name="frame" value="0" />
            </conditional>
            <param name="download_tar" value="false" />
            <output_collection name="output_file" type="list">
                <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" file="test0.tiff"/>
            </output_collection>
        </test>
        <test expect_failure="true">
            <conditional name="omero_instance_type">
                 <param name="omero_instance" value="priv" />

            <param name="download_tar" value="false" />
            <assert_stderr>
                <has_text text="OMERO connection credentials are empty. Set your credentials via: User -> Preferences -> Manage Information" />
            </assert_stderr >
        </test>
        <test>
            <conditional name="omero_instance_type">
                 <param name="omero_instance" value="idr" />
            </conditional>
            <!-- Test for download all images from a dataset -->
            <param name="source" value="omeroDatasetID" />
            <param name="id_dataset_omero" value="9059" />
            <param name="download_tar" value="false" />
            <output_collection name="output_file" type="list" count="4">
                <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024">
                    <assert_contents>
                        <has_size value="2097286" />
                    </assert_contents>
                </element>
                <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_D3D__9036708__0__0__1024__1024">
                    <assert_contents>
                        <has_size value="2097286" />
                    </assert_contents>
                </element>
                <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_D3D_zproj__9036710__0__0__1024__1024">
                    <assert_contents>
                        <has_size value="2097286" />
                    </assert_contents>
                </element>
                <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_REF__9036709__0__0__1024__1024">
                    <assert_contents>
                        <has_size value="2097286" />
                    </assert_contents>
                </element>
            </output_collection>
        </test>
        <test>
            <conditional name="omero_instance_type">
                 <param name="omero_instance" value="idr" />
            </conditional>
            <!-- Test for download all original files from a dataset -->
            <!-- Impossible in idr: -->

            <param name="download_tar" value="false" />
            <conditional name="image_region">
                <param name="original" value="original"/> 
            </conditional>
            <output_collection name="output_file" type="list" count="0">
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
Download image data from the IDR_ (Image Data Resource) - a public repository

13:f92941d1a85e

<?xml version="1.0"?>
<tool id="idr_download_by_ids" name="Download IDR/OMERO" version="0.45" profile="18.09">
    <description></description>
    <macros>
        <xml name="region_spec" token_pos="upper-left corner">
            <param name="x_coord" type="integer" value="0" min="0"
            label="x-coordinate of region @POS@" />

    </macros>
    <edam_operations>
        <edam_operation>operation_3443</edam_operation>
    </edam_operations>
    <requirements>
        <requirement type="package" version="5.19.4">omero-py</requirement>
        <requirement type="package" version="2024.9.20">tifffile</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        
        #if $omero_instance_type.omero_instance == "priv":
            ## the user wants to use a non-public OMERO instance

        #if str($image_ids.source) == 'omeroDatasetID':
            --dataset
        #end if
        #if $image_region.original == "original":
            --download-original
        #elif $image_region.original == "full":
            --download-full
        #else:
            #set $channel = str($image_region.channel).strip()
            #if $channel:
                -c '$channel'
            #end if

    "username": "$username",
    "password": "$password"
}
        ]]></configfile>
    </configfiles>
    <inputs>
        <conditional name="omero_instance_type">
            <param name="omero_instance" type="select" label="Which OMERO instance to connect?"
                   help="By default, the tool will download a tarball containing individual images from IDR into your Galaxy history. If you 
                   need to connect to your own instance, set your connection username and password from User->Preference->Manage Information" >
                <option value="idr">IDR</option>

        </conditional>

        <conditional name="image_region">
            <param name="original" type="select" label="Which images do you want to download?">
                <option value="TIFF" selected="true">Exported TIFF (single channel, single stack)</option>
                <option value="full">Whole TIFF (all channels, all frames, all stacks)</option>
                <option value="original">Original file (file uploaded to omero, only available for private instances)</option>
            </param>
            <when value="original"/>
            <when value="full"/>
            <when value="TIFF">
                <param name="channel" type="text"
                    label="Name of the channel to download"
                    help="For all image IDs only the specified channel will be downloaded. If left empty, the first channel (whatever this is) will be downloaded by default." />
                <param name="z_section" type="integer" value="0" min="0"

        <data name="output_tar" format="tar" from_work_dir="./downloads/images.tar" label ="Images tarball">
            <filter>download_tar</filter>
        </data> 
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <conditional name="omero_instance_type">
                 <param name="omero_instance" value="idr" />
            </conditional>
            <param name="source" value="dataset" />
            <param name="id_spec" value="ids.txt" />

                </conditional>
                <param name="frame" value="0" />
            </conditional>
            <param name="download_tar" value="false" />
            <output_collection name="output_file" type="list">
                <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test0.tiff" compare="image_diff" />
            </output_collection>
        </test>
        <test expect_num_outputs="2">
            <conditional name="omero_instance_type">
                 <param name="omero_instance" value="idr" />
            </conditional>
            <param name="source" value="link" />
            <param name="id_spec" value="1884807" />

                </conditional>
                <param name="frame" value="2" />
            </conditional>
            <param name="download_tar" value="false" />
            <output_collection name="output_file" type="list">
                <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test1.tiff" compare="image_diff"/>
            </output_collection>
        </test>
        <test expect_num_outputs="2">
            <conditional name="omero_instance_type">
                 <param name="omero_instance" value="idr" />
            </conditional>
            <param name="source" value="link" />
            <param name="id_spec" value="1884807" />

                </conditional>
                <param name="frame" value="2" />
            </conditional>
            <param name="download_tar" value="false" />
            <output_collection name="output_file" type="list">
                <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test2.tiff" compare="image_diff"/>
            </output_collection>
        </test>
        <test expect_num_outputs="2">
            <conditional name="omero_instance_type">
                 <param name="omero_instance" value="idr" />
            </conditional>
            <param name="source" value="link" />
            <param name="id_spec" value="https://idr.openmicroscopy.org/webclient/?show=image-9036708|image-9036710|image-9036711" />

            </conditional>
            <param name="download_tar" value="false" />
            <output_collection name="output_file" type="list" count="3">
                <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024">
                    <assert_contents>
                        <has_size size="2097286" />
                        <has_image_width width="1024" />
                        <has_image_height height="1024" />
                        <has_image_mean_intensity mean_intensity="320.868" />
                        <has_image_center_of_mass center_of_mass="541.664, 456.743" />
                    </assert_contents>
                </element>
            </output_collection>
            <output name="out_log">
                <assert_contents>

                </conditional>
                <param name="frame" value="20" />
            </conditional>
            <param name="download_tar" value="false" />
        </test>
        <test expect_num_outputs="2">
            <!-- Repeat test with non-existing image-ID 9036708999,
            but use skip-failed option -->
            <conditional name="omero_instance_type">
                 <param name="omero_instance" value="idr" />
            </conditional>

            <param name="skip_failed" value="true" />
            <param name="download_tar" value="false" />
            <output_collection name="output_file" type="list" count="2">
                <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024">
                    <assert_contents>
                        <has_size size="2097286" />
                        <has_image_width width="1024" />
                        <has_image_height height="1024" />
                        <has_image_mean_intensity mean_intensity="320.868" />
                        <has_image_center_of_mass center_of_mass="541.664, 456.743" />
                    </assert_contents>
                </element>
            </output_collection>
            <output name="out_log">
                <assert_contents>

                    <has_text text="(ID: 9036710): Specified image plane (4) is out of bounds" />
                    <has_n_lines n="2"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="2">
            <conditional name="omero_instance_type">
                 <param name="omero_instance" value="idr" />
            </conditional>
            <!-- Test for download images in a tarball -->
            <param name="source" value="dataset" />

                </conditional>
                <param name="frame" value="0" />
            </conditional>
            <output name="output_tar">
                    <assert_contents>
                        <has_size size="1382400" />
                        <has_archive_member path=".*/*__1828167__0__0__671__511.tiff" >
                            <has_size size="685896" />
                            <has_image_width width="671" />
                            <has_image_height height="511" />
                            <has_image_mean_intensity mean_intensity="388.711" />
                            <has_image_center_of_mass center_of_mass="354.627, 267" />
                        </has_archive_member>
                        <has_archive_member path=".*/*__1828658__0__0__671__511.tiff" >
                            <has_size size="685896" />
                            <has_image_width width="671" />
                            <has_image_height height="511" />
                            <has_image_mean_intensity mean_intensity="397.507" />
                            <has_image_center_of_mass center_of_mass="346.098, 250.652" />
                        </has_archive_member>
                    </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="2">
            <conditional name="omero_instance_type">
                 <param name="omero_instance" value="priv" />
                 <param name="omero_host" value="idr.openmicroscopy.org" />
                 <param name="omero_secured" value="true" />
                 <param name="galaxy_test_param" value="true" />

                </conditional>
                <param name="frame" value="0" />
            </conditional>
            <param name="download_tar" value="false" />
            <output_collection name="output_file" type="list">
                <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" file="test0.tiff" compare="image_diff"/>
            </output_collection>
        </test>
        <test expect_failure="true">
            <conditional name="omero_instance_type">
                 <param name="omero_instance" value="priv" />

            <param name="download_tar" value="false" />
            <assert_stderr>
                <has_text text="OMERO connection credentials are empty. Set your credentials via: User -> Preferences -> Manage Information" />
            </assert_stderr >
        </test>
        <test expect_num_outputs="2">
            <conditional name="omero_instance_type">
                 <param name="omero_instance" value="idr" />
            </conditional>
            <!-- Test for download all images from a dataset -->
            <param name="source" value="omeroDatasetID" />
            <param name="id_dataset_omero" value="9059" />
            <param name="download_tar" value="false" />
            <output_collection name="output_file" type="list" count="4">
                <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024">
                    <assert_contents>
                        <has_size size="2097286" />
                        <has_image_width width="1024" />
                        <has_image_height height="1024" />
                        <has_image_mean_intensity mean_intensity="145.310" />
                        <has_image_center_of_mass center_of_mass="527.499, 480.704" />
                    </assert_contents>
                </element>
                <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_D3D__9036708__0__0__1024__1024">
                    <assert_contents>
                        <has_size size="2097286" />
                        <has_image_width width="1024" />
                        <has_image_height height="1024" />
                        <has_image_mean_intensity mean_intensity="147.025" />
                        <has_image_center_of_mass center_of_mass="528.977, 480.691" />
                    </assert_contents>
                </element>
                <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_D3D_zproj__9036710__0__0__1024__1024">
                    <assert_contents>
                        <has_size size="2097286" />
                        <has_image_width width="1024" />
                        <has_image_height height="1024" />
                        <has_image_mean_intensity mean_intensity="210.787" />
                        <has_image_center_of_mass center_of_mass="534.629, 473.267" />
                    </assert_contents>
                </element>
                <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_REF__9036709__0__0__1024__1024">
                    <assert_contents>
                        <has_size size="2097286" />
                        <has_image_width width="1024" />
                        <has_image_height height="1024" />
                        <has_image_mean_intensity mean_intensity="3816.051" />
                        <has_image_center_of_mass center_of_mass="512.274, 503.186" />
                    </assert_contents>
                </element>
            </output_collection>
        </test>
        <test expect_num_outputs="2">
            <conditional name="omero_instance_type">
                 <param name="omero_instance" value="idr" />
            </conditional>
            <!-- Test for download all original files from a dataset -->
            <!-- Impossible in idr: -->

            <param name="download_tar" value="false" />
            <conditional name="image_region">
                <param name="original" value="original"/> 
            </conditional>
            <output_collection name="output_file" type="list" count="0">
            </output_collection>
        </test>
        <test expect_num_outputs="2">
            <conditional name="omero_instance_type">
                 <param name="omero_instance" value="idr" />
            </conditional>
            <param name="source" value="link" />
            <param name="id_spec" value="1229801" />
            <param name="download_tar" value="false" />
            <conditional name="image_region">
                <param name="original" value="full"/> 
            </conditional>
            <output_collection name="output_file" type="list" count="1">
                <element name="JL_120731_S6A_[Well_A-1;_Field_#1]__1229801__full">
                    <assert_contents>
                        <has_size size="91592058" />
                    </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
Download image data from the IDR_ (Image Data Resource) - a public repository