Mercurial > repos > iuc > idr_download_by_ids

comparison idr_download_by_ids.xml @ 10:4aed70472589 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
author iuc
date Wed, 24 Nov 2021 21:01:02 +0000
parents 80af973c5277
children cbd605a24336
comparison
equal deleted inserted replaced
9:80af973c5277 10:4aed70472589
14 label="Region height" 14 label="Region height"
15 help="Set to zero to extend the rectangle maximally along the y-axis of the image" /> 15 help="Set to zero to extend the rectangle maximally along the y-axis of the image" />
16 </xml> 16 </xml>
17 </macros> 17 </macros>
18 <requirements> 18 <requirements>
19 <requirement type="package" version="5.7.1">python-omero</requirement> 19 <requirement type="package" version="5.10.1">omero-py</requirement>
20 <requirement type="package" version="0.4.2">pylibtiff</requirement> 20 <requirement type="package" version="0.4.2">pylibtiff</requirement>
21 </requirements> 21 </requirements>
22 <command detect_errors="exit_code"><![CDATA[ 22 <command detect_errors="exit_code"><![CDATA[
23 23
24 #if $omero_instance_type.omero_instance == "priv": 24 #if $omero_instance_type.omero_instance == "priv":
35 35
36 mkdir downloads && cd downloads && 36 mkdir downloads && cd downloads &&
37 #if str($image_ids.source) == 'link': 37 #if str($image_ids.source) == 'link':
38 python -c 'print("${image_ids.id_spec}".replace(",", "|").split("?show=")[-1].replace("|", "\n"))' 38 python -c 'print("${image_ids.id_spec}".replace(",", "|").split("?show=")[-1].replace("|", "\n"))'
39 ## https://idr.openmicroscopy.org/webclient/?show=image-3426274|image-3426275|image-3426276|image-3426277 39 ## https://idr.openmicroscopy.org/webclient/?show=image-3426274|image-3426275|image-3426276|image-3426277
40 #elif str($image_ids.source) == 'dataset':
41 cat '${image_ids.id_spec}'
40 #else: 42 #else:
41 cat '${image_ids.id_spec}' 43 echo '${image_ids.id_dataset_omero}'
42 #end if 44 #end if
43 | python '$__tool_directory__/idr_download_by_ids.py' 45 | python '$__tool_directory__/idr_download_by_ids.py'
46 #if str($image_ids.source) == 'omeroDatasetID':
47 --dataset
48 #end if
44 #set $channel = str($channel).strip() 49 #set $channel = str($channel).strip()
45 #if $channel: 50 #if $channel:
46 -c '$channel' 51 -c '$channel'
47 #end if 52 #end if
48 -f $frame 53 -f $frame
98 103
99 <conditional name="image_ids"> 104 <conditional name="image_ids">
100 <param name="source" type="select" label="How would you like to specify the IDs of images to download?"> 105 <param name="source" type="select" label="How would you like to specify the IDs of images to download?">
101 <option value="link">As text (comma-separated list of IDs or a valid IDR link)</option> 106 <option value="link">As text (comma-separated list of IDs or a valid IDR link)</option>
102 <option value="dataset">As a dataset (one image ID per line)</option> 107 <option value="dataset">As a dataset (one image ID per line)</option>
108 <option value="omeroDatasetID">All images from a single Dataset ID</option>
103 </param> 109 </param>
104 <when value="link"> 110 <when value="link">
105 <param name="id_spec" type="text" 111 <param name="id_spec" type="text"
106 label="Image IDs to download" 112 label="Image IDs to download"
107 help="You can enter a single image-id, or a comma (or '|')-separated list of IDs. Alternatively, you can paste here a link to an image selection obtained through the IDR webclient."> 113 help="You can enter a single image-id, or a comma (or '|')-separated list of IDs. Alternatively, you can paste here a link to an image selection obtained through the IDR webclient.">
111 </param> 117 </param>
112 </when> 118 </when>
113 <when value="dataset"> 119 <when value="dataset">
114 <param name="id_spec" type="data" format="txt" 120 <param name="id_spec" type="data" format="txt"
115 label="Select a dataset with image IDs (one per line)" /> 121 label="Select a dataset with image IDs (one per line)" />
122 </when>
123 <when value="omeroDatasetID">
124 <param name="id_dataset_omero" type="integer" min = "0" value = "9059" label="Dataset ID"/>
116 </when> 125 </when>
117 </conditional> 126 </conditional>
118 <param name="channel" type="text" 127 <param name="channel" type="text"
119 label="Name of the channel to download" 128 label="Name of the channel to download"
120 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." /> 129 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." />
360 <param name="download_tar" value="false" /> 369 <param name="download_tar" value="false" />
361 <assert_stderr> 370 <assert_stderr>
362 <has_text text="OMERO connection credentials are empty. Set your credentials via: User -> Preferences -> Manage Information" /> 371 <has_text text="OMERO connection credentials are empty. Set your credentials via: User -> Preferences -> Manage Information" />
363 </assert_stderr > 372 </assert_stderr >
364 </test> 373 </test>
374 <test>
375 <conditional name="omero_instance_type">
376 <param name="omero_instance" value="idr" />
377 </conditional>
378 <!-- Test for download all images from a dataset -->
379 <param name="source" value="omeroDatasetID" />
380 <param name="id_dataset_omero" value="9059" />
381 <param name="download_tar" value="false" />
382 <output_collection name="output_file" type="list" count="4">
383 <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024">
384 <assert_contents>
385 <has_size value="2097286" />
386 </assert_contents>
387 </element>
388 <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_D3D__9036708__0__0__1024__1024">
389 <assert_contents>
390 <has_size value="2097286" />
391 </assert_contents>
392 </element>
393 <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_D3D_zproj__9036710__0__0__1024__1024">
394 <assert_contents>
395 <has_size value="2097286" />
396 </assert_contents>
397 </element>
398 <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_REF__9036709__0__0__1024__1024">
399 <assert_contents>
400 <has_size value="2097286" />
401 </assert_contents>
402 </element>
403 </output_collection>
404 </test>
365 </tests> 405 </tests>
366 <help><![CDATA[ 406 <help><![CDATA[
367 Download image data from the IDR_ (Image Data Resource) - a public repository 407 Download image data from the IDR_ (Image Data Resource) - a public repository
368 of reference image datasets from published scientific studies. 408 of reference image datasets from published scientific studies.
369 409
388 https://idr.openmicroscopy.org/webclient/?show=image-9036708|image-9036710|image-9036711 428 https://idr.openmicroscopy.org/webclient/?show=image-9036708|image-9036710|image-9036711
389 429
390 Alternatively, you can simply provide a list of known image IDs in the text 430 Alternatively, you can simply provide a list of known image IDs in the text
391 input field (comma or '|'-separated ), or as an input file (each ID on a 431 input field (comma or '|'-separated ), or as an input file (each ID on a
392 separate line). 432 separate line).
433
434 Finally, if you want to download all images of a single dataset. Specify the id as
435 All images from a single Dataset ID.
393 436
394 Most images in the IDR have more than two dimensions. Thus, there are 437 Most images in the IDR have more than two dimensions. Thus, there are
395 parameters available which allow you to select a particular recording channel, 438 parameters available which allow you to select a particular recording channel,
396 z-plane or time frame to download. 439 z-plane or time frame to download.
397 You can also select a region which will be used to crop the images, rather 440 You can also select a region which will be used to crop the images, rather