Mercurial > repos > iuc > idr_download_by_ids
changeset 7:f067504aa92a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
| author | iuc |
|---|---|
| date | Thu, 05 Nov 2020 23:29:40 +0000 |
| parents | 5c743356df83 |
| children | 97f70f7ed077 |
| files | README.md idr_download_by_ids.py idr_download_by_ids.xml test-data/test0.tiff |
| diffstat | 4 files changed, 113 insertions(+), 28 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Thu Nov 05 23:29:40 2020 +0000 @@ -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 +```
--- 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 @@ -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()
--- 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 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="idr_download_by_ids" name="IDR Download" version="0.42" profile="18.09"> +<tool id="idr_download_by_ids" name="IDR Download" version="0.43" profile="18.09"> <description>- download images from the Image Data Resource using image IDs</description> <macros> <xml name="region_spec" token_pos="upper-left corner"> @@ -16,10 +16,21 @@ </xml> </macros> <requirements> - <requirement type="package" version="5.6.0">python-omero</requirement> + <requirement type="package" version="5.7.1">python-omero</requirement> <requirement type="package" version="0.4.2">pylibtiff</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ + + #if $omero_instance_type.omero_instance == "priv": + #set $username = $__user__.extra_preferences.get('omero_account|username', "") + #set $password = $__user__.extra_preferences.get('omero_account|password', "") + + #if $username == "" or $password =="": + echo "OMERO connection credentials are empty. Set your credentials via: User -> Preferences -> Manage Information" && + exit 1 + #end if + #end if + mkdir downloads && cd downloads && #if str($image_ids.source) == 'link': python -c 'print("${image_ids.id_spec}".replace(",", "|").split("?show=")[-1].replace("|", "\n"))' @@ -39,10 +50,35 @@ #end if $skip_failed $download_tar - + #if $omero_instance_type.omero_instance =='priv': + -h '$omero_host' + $omero_secured + -u '$username' + -p '$password' + #end if 2> >(tee -a $out_log >&2) ]]></command> <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> + <option value="priv">other OMERO instance</option> + </param> + <when value="priv"> + <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> + </param> + <param name="omero_secured" type="boolean" label="Seured connection?" checked="true" truevalue="--omero-secured" falsevalue="" + help="Select Yes if your OMERO instance is running with SSL, otherwise select No"> + </param> + </when> + <when value="idr" /> + </conditional> + <conditional name="image_ids"> <param name="source" type="select" label="How would you like to specify the IDs of images to download?"> <option value="link">As text (comma-separated list of IDs or a valid IDR link)</option> @@ -104,9 +140,32 @@ </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" /> - <param name="channel" value="615.0" /> + <param name="channel" value="PCNT" /> + <conditional name="clip_image"> + <param name="select" value="--rectangle" /> + <param name="x_coord" value="3" /> + <param name="y_coord" value="3" /> + <param name="width" value="5" /> + <param name="height" value="5" /> + </conditional> + <param name="frame" value="0" /> + <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> + <conditional name="omero_instance_type"> + <param name="omero_instance" value="idr" /> + </conditional> + <param name="source" value="link" /> + <param name="id_spec" value="1884807" /> + <param name="channel" value="PCNT" /> <conditional name="clip_image"> <param name="select" value="--rectangle" /> <param name="x_coord" value="3" /> @@ -121,26 +180,12 @@ </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" /> - <param name="channel" value="615.0" /> - <conditional name="clip_image"> - <param name="select" value="--rectangle" /> - <param name="x_coord" value="3" /> - <param name="y_coord" value="3" /> - <param name="width" value="5" /> - <param name="height" value="5" /> - </conditional> - <param name="frame" value="2" /> - <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="test1.tiff"/> - </output_collection> - </test> - <test> - <param name="source" value="link" /> - <param name="id_spec" value="1884807" /> - <param name="channel" value="615.0" /> + <param name="channel" value="PCNT" /> <conditional name="clip_image"> <param name="select" value="--center" /> <param name="x_coord" value="5" /> @@ -155,6 +200,9 @@ </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" /> <param name="channel" value="Spo20(51-91)" /> @@ -179,6 +227,9 @@ </output> </test> <test expect_failure="true"> + <conditional name="omero_instance_type"> + <param name="omero_instance" value="idr" /> + </conditional> <!-- Test behavior with non-existing image-ID 9036708999 --> <param name="source" value="link" /> <param name="id_spec" value="https://idr.openmicroscopy.org/webclient/?show=image-9036708999|image-9036710|image-9036711" /> @@ -193,6 +244,9 @@ <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="source" value="link" /> <param name="id_spec" value="https://idr.openmicroscopy.org/webclient/?show=image-9036708999|image-9036710|image-9036711" /> <param name="channel" value="Spo20(51-91)" /> @@ -219,6 +273,9 @@ </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" /> <param name="id_spec" value="ids_tar.txt" />