| Previous changeset 6:5c743356df83 (2020-07-06) Next changeset 8:97f70f7ed077 (2020-11-22) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d" |
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modified:
idr_download_by_ids.py idr_download_by_ids.xml |
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added:
README.md test-data/test0.tiff |
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| diff -r 5c743356df83 -r f067504aa92a README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Thu Nov 05 23:29:40 2020 +0000 |
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| @@ -0,0 +1,18 @@ +## Set up user credentials on Galaxy to connect to other omero instance + +To enable users to set their credentials for this tool, +make sure the file `config/user_preferences_extra.yml` has the following section: + +``` + omero_account: + description: Your OMERO instance connection credentials + inputs: + - name: username + label: Username + type: text + required: False + - name: password + label: Password + type: password + required: False +``` |
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| diff -r 5c743356df83 -r f067504aa92a idr_download_by_ids.py --- a/idr_download_by_ids.py Mon Jul 06 19:33:59 2020 -0400 +++ b/idr_download_by_ids.py Thu Nov 05 23:29:40 2020 +0000 |
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| @@ -112,7 +112,7 @@ image_ids, channel=None, z_stack=0, frame=0, coord=(0, 0), width=0, height=0, region_spec='rectangle', - skip_failed=False, download_tar=False + skip_failed=False, download_tar=False, omero_host='idr.openmicroscopy.org', omero_secured=True, omero_username='public', omero_password='public' ): # basic argument sanity checks and adjustments prefix = 'image-' @@ -127,14 +127,12 @@ 'Got unknown value "{0}" as region_spec argument' .format(region_spec) ) - with ExitStack() as exit_stack: - # connect to idr conn = exit_stack.enter_context( BlitzGateway( - 'public', 'public', - host='idr.openmicroscopy.org', - secure=True + omero_username, omero_password, + host=omero_host, + secure=omero_secured ) ) # exit_stack.callback(conn.connect().close) @@ -356,6 +354,18 @@ p.add_argument( '--download-tar', action='store_true' ) + p.add_argument( + '-oh', '--omero-host', type=str, default="idr.openmicroscopy.org" + ) + p.add_argument( + '--omero-secured', action='store_false' + ) + p.add_argument( + '-u', '--omero-username', type=str, default="public" + ) + p.add_argument( + '-p', '--omero-password', type=str, default="public" + ) args = p.parse_args() if not args.image_ids: args.image_ids = sys.stdin.read().split() |
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| diff -r 5c743356df83 -r f067504aa92a idr_download_by_ids.xml --- a/idr_download_by_ids.xml Mon Jul 06 19:33:59 2020 -0400 +++ b/idr_download_by_ids.xml Thu Nov 05 23:29:40 2020 +0000 |
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| b'@@ -1,5 +1,5 @@\n <?xml version="1.0"?>\n-<tool id="idr_download_by_ids" name="IDR Download" version="0.42" profile="18.09">\n+<tool id="idr_download_by_ids" name="IDR Download" version="0.43" profile="18.09">\n <description>- download images from the Image Data Resource using image IDs</description>\n <macros>\n <xml name="region_spec" token_pos="upper-left corner">\n@@ -16,10 +16,21 @@\n </xml>\n </macros>\n <requirements>\n- <requirement type="package" version="5.6.0">python-omero</requirement>\n+ <requirement type="package" version="5.7.1">python-omero</requirement>\n <requirement type="package" version="0.4.2">pylibtiff</requirement>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[\n+ \n+ #if $omero_instance_type.omero_instance == "priv":\n+ #set $username = $__user__.extra_preferences.get(\'omero_account|username\', "")\n+ #set $password = $__user__.extra_preferences.get(\'omero_account|password\', "")\n+\n+ #if $username == "" or $password =="":\n+ echo "OMERO connection credentials are empty. Set your credentials via: User -> Preferences -> Manage Information" &&\n+ exit 1\n+ #end if\n+ #end if\n+ \n mkdir downloads && cd downloads &&\n #if str($image_ids.source) == \'link\':\n python -c \'print("${image_ids.id_spec}".replace(",", "|").split("?show=")[-1].replace("|", "\\n"))\'\n@@ -39,10 +50,35 @@\n #end if\n $skip_failed\n $download_tar\n-\n+ #if $omero_instance_type.omero_instance ==\'priv\':\n+ -h \'$omero_host\'\n+ $omero_secured\n+ -u \'$username\'\n+ -p \'$password\'\n+ #end if\n 2> >(tee -a $out_log >&2)\n ]]></command>\n <inputs>\n+ <conditional name="omero_instance_type">\n+ <param name="omero_instance" type="select" label="Which OMERO instance to connect?"\n+ help="By default, the tool will download a tarball containing individual images from IDR into your Galaxy history. If you \n+ need to connect to your own instance, set your connection username and password from User->Preference->Manage Information" >\n+ <option value="idr">IDR</option>\n+ <option value="priv">other OMERO instance</option>\n+ </param>\n+ <when value="priv">\n+ <param name="omero_host" type="text" label="OMERO host URL">\n+ <validator type="regex" message="Enter a valid host location, for example, your.omero.server">\n+ [.A-Za-z0-9_-]\n+ </validator>\n+ </param>\n+ <param name="omero_secured" type="boolean" label="Seured connection?" checked="true" truevalue="--omero-secured" falsevalue=""\n+ help="Select Yes if your OMERO instance is running with SSL, otherwise select No">\n+ </param>\n+ </when>\n+ <when value="idr" />\n+ </conditional>\n+\n <conditional name="image_ids">\n <param name="source" type="select" label="How would you like to specify the IDs of images to download?">\n <option value="link">As text (comma-separated list of IDs or a valid IDR link)</option>\n@@ -104,9 +140,32 @@\n </outputs>\n <tests>\n <test>\n+ <conditional name="omero_instance_type">\n+ <param name="omero_instance" value="idr" />\n+ </conditional>\n <param name="source" value="dataset" />\n <param name="id_spec" value="ids.txt" />\n- <param name="channel" value="615.0" />\n+ <param name="channel" value="PCNT" />\n+ <conditional name="clip_image">\n+ <param name="select" value="--rectangle" />\n+ <param name="x_coord" value="3" />\n+ <param name="y_coord" value="3" />\n+ <param name='..b' <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" file="test0.tiff"/>\n+ </output_collection>\n+ </test>\n+ <test>\n+ <conditional name="omero_instance_type">\n+ <param name="omero_instance" value="idr" />\n+ </conditional>\n+ <param name="source" value="link" />\n+ <param name="id_spec" value="1884807" />\n+ <param name="channel" value="PCNT" />\n <conditional name="clip_image">\n <param name="select" value="--rectangle" />\n <param name="x_coord" value="3" />\n@@ -121,26 +180,12 @@\n </output_collection>\n </test>\n <test>\n+ <conditional name="omero_instance_type">\n+ <param name="omero_instance" value="idr" />\n+ </conditional>\n <param name="source" value="link" />\n <param name="id_spec" value="1884807" />\n- <param name="channel" value="615.0" />\n- <conditional name="clip_image">\n- <param name="select" value="--rectangle" />\n- <param name="x_coord" value="3" />\n- <param name="y_coord" value="3" />\n- <param name="width" value="5" />\n- <param name="height" value="5" />\n- </conditional>\n- <param name="frame" value="2" />\n- <param name="download_tar" value="false" />\n- <output_collection name="output_file" type="list">\n- <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" file="test1.tiff"/>\n- </output_collection>\n- </test>\n- <test>\n- <param name="source" value="link" />\n- <param name="id_spec" value="1884807" />\n- <param name="channel" value="615.0" />\n+ <param name="channel" value="PCNT" />\n <conditional name="clip_image">\n <param name="select" value="--center" />\n <param name="x_coord" value="5" />\n@@ -155,6 +200,9 @@\n </output_collection>\n </test>\n <test>\n+ <conditional name="omero_instance_type">\n+ <param name="omero_instance" value="idr" />\n+ </conditional>\n <param name="source" value="link" />\n <param name="id_spec" value="https://idr.openmicroscopy.org/webclient/?show=image-9036708|image-9036710|image-9036711" />\n <param name="channel" value="Spo20(51-91)" />\n@@ -179,6 +227,9 @@\n </output>\n </test>\n <test expect_failure="true">\n+ <conditional name="omero_instance_type">\n+ <param name="omero_instance" value="idr" />\n+ </conditional>\n <!-- Test behavior with non-existing image-ID 9036708999 -->\n <param name="source" value="link" />\n <param name="id_spec" value="https://idr.openmicroscopy.org/webclient/?show=image-9036708999|image-9036710|image-9036711" />\n@@ -193,6 +244,9 @@\n <test>\n <!-- Repeat test with non-existing image-ID 9036708999,\n but use skip-failed option -->\n+ <conditional name="omero_instance_type">\n+ <param name="omero_instance" value="idr" />\n+ </conditional>\n <param name="source" value="link" />\n <param name="id_spec" value="https://idr.openmicroscopy.org/webclient/?show=image-9036708999|image-9036710|image-9036711" />\n <param name="channel" value="Spo20(51-91)" />\n@@ -219,6 +273,9 @@\n </output>\n </test>\n <test>\n+ <conditional name="omero_instance_type">\n+ <param name="omero_instance" value="idr" />\n+ </conditional>\n <!-- Test for download images in a tarball -->\n <param name="source" value="dataset" />\n <param name="id_spec" value="ids_tar.txt" />\n' |
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| diff -r 5c743356df83 -r f067504aa92a test-data/test0.tiff |
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| Binary file test-data/test0.tiff has changed |