Mercurial > repos > iuc > idr_download_by_ids

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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 a9a143bae95eb6c553fd3d5955c2adb34352480f
author iuc
date Thu, 26 Sep 2024 12:32:17 +0000
parents 4b794652dcdc
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
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diff changeset
1 <?xml version="1.0"?>
13
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
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2 <tool id="idr_download_by_ids" name="Download IDR/OMERO" version="0.45" profile="18.09">
12
4b794652dcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 18d21cc8fc24236c514ffe31332bfa13cd08d1e9
iuc
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3 <description></description>
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57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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4 <macros>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
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5 <xml name="region_spec" token_pos="upper-left corner">
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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6 <param name="x_coord" type="integer" value="0" min="0"
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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7 label="x-coordinate of region @POS@" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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8 <param name="y_coord" type="integer" value="0" min="0"
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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9 label="y-coordinate of region @POS@" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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10 <param name="width" type="integer" value="0" min="0"
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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11 label="Region width"
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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12 help="Set to zero to extend the rectangle maximally along the x-axis of the image" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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13 <param name="height" type="integer" value="0" min="0"
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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14 label="Region height"
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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15 help="Set to zero to extend the rectangle maximally along the y-axis of the image" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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16 </xml>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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17 </macros>
12
4b794652dcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 18d21cc8fc24236c514ffe31332bfa13cd08d1e9
iuc
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18 <edam_operations>
4b794652dcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 18d21cc8fc24236c514ffe31332bfa13cd08d1e9
iuc
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19 <edam_operation>operation_3443</edam_operation>
4b794652dcdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 18d21cc8fc24236c514ffe31332bfa13cd08d1e9
iuc
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20 </edam_operations>
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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21 <requirements>
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f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
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22 <requirement type="package" version="5.19.4">omero-py</requirement>
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
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23 <requirement type="package" version="2024.9.20">tifffile</requirement>
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57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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24 </requirements>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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25 <command detect_errors="exit_code"><![CDATA[
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f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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27 #if $omero_instance_type.omero_instance == "priv":
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28 ## the user wants to use a non-public OMERO instance
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
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29 ## check if credentials are set in the user-preferences, if not warn the user and exit
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f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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30 #set $username = $__user__.extra_preferences.get('omero_account|username', "")
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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31 #set $password = $__user__.extra_preferences.get('omero_account|password', "")
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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32
8
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33 #if $omero_instance_type.galaxy_test_param != 'true' and ($username == "" or $password ==""):
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
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34 echo "OMERO connection credentials are empty. Set your credentials via: User -> Preferences -> Manage Information" 1>&2 &&
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
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35 exit 1 &&
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f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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36 #end if
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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37 #end if
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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38
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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39 mkdir downloads && cd downloads &&
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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40 #if str($image_ids.source) == 'link':
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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41 python -c 'print("${image_ids.id_spec}".replace(",", "|").split("?show=")[-1].replace("|", "\n"))'
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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42 ## https://idr.openmicroscopy.org/webclient/?show=image-3426274|image-3426275|image-3426276|image-3426277
10
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
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43 #elif str($image_ids.source) == 'dataset':
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
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44 cat '${image_ids.id_spec}'
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45 #else:
10
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
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46 echo '${image_ids.id_dataset_omero}'
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47 #end if
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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48 | python '$__tool_directory__/idr_download_by_ids.py'
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4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
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49 #if str($image_ids.source) == 'omeroDatasetID':
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
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50 --dataset
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
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51 #end if
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cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
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52 #if $image_region.original == "original":
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
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53 --download-original
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f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
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54 #elif $image_region.original == "full":
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
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55 --download-full
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cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
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56 #else:
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
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57 #set $channel = str($image_region.channel).strip()
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
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58 #if $channel:
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
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59 -c '$channel'
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
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60 #end if
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
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61 -f $image_region.frame
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
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62 -z $image_region.z_section
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
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63 #if str($image_region.clip_image.select):
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
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64 ${image_region.clip_image.select} ${image_region.clip_image.x_coord} ${image_region.clip_image.y_coord} ${image_region.clip_image.width} ${image_region.clip_image.height}
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
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65 #end if
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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66 #end if
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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67 $skip_failed
4
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
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68 $download_tar
7
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69 #if $omero_instance_type.omero_instance =='priv':
8
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70 -oh '$omero_instance_type.omero_host'
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
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71 $omero_instance_type.omero_secured
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
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72 -cf '$credentials'
7
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73 #end if
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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74 2> >(tee -a $out_log >&2)
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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75 ]]></command>
8
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
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76 <configfiles>
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
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77 <configfile name="credentials"><![CDATA[
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
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78 #if $omero_instance_type.omero_instance =='priv' and $omero_instance_type.galaxy_test_param == 'true':
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
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79 ## as a test for a private instance we actually use a public instance, but with credentials
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
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80 #set $username = 'public'
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
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81 #set $password = 'public'
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
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82 #else:
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
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83 #set $username = $__user__.extra_preferences.get('omero_account|username', "")
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84 #set $password = $__user__.extra_preferences.get('omero_account|password', "")
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85 #end if
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86 {
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87 "username": "$username",
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88 "password": "$password"
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89 }
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90 ]]></configfile>
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91 </configfiles>
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92 <inputs>
7
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93 <conditional name="omero_instance_type">
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94 <param name="omero_instance" type="select" label="Which OMERO instance to connect?"
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95 help="By default, the tool will download a tarball containing individual images from IDR into your Galaxy history. If you
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96 need to connect to your own instance, set your connection username and password from User->Preference->Manage Information" >
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97 <option value="idr">IDR</option>
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98 <option value="priv">other OMERO instance</option>
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99 </param>
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100 <when value="priv">
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101 <param name="omero_host" type="text" label="OMERO host URL">
8
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102 <validator type="regex" message="Enter a valid host location, for example, your.omero.server">^[a-zA-Z0-9._-]*$</validator>
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103 <validator type="expression" message="No two dots (..) allowed">'..' not in value</validator>
7
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104 </param>
8
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105 <param name="omero_secured" type="boolean" label="Secured connection?" checked="true" truevalue="--omero-secured" falsevalue=""
7
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106 help="Select Yes if your OMERO instance is running with SSL, otherwise select No">
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107 </param>
8
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108 <param name="galaxy_test_param" type="hidden" value="false" />
7
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109 </when>
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110 <when value="idr" />
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111 </conditional>
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112
0
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113 <conditional name="image_ids">
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114 <param name="source" type="select" label="How would you like to specify the IDs of images to download?">
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115 <option value="link">As text (comma-separated list of IDs or a valid IDR link)</option>
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116 <option value="dataset">As a dataset (one image ID per line)</option>
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117 <option value="omeroDatasetID">All images from a single Dataset ID</option>
0
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118 </param>
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119 <when value="link">
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120 <param name="id_spec" type="text"
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121 label="Image IDs to download"
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122 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.">
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123 <sanitizer>
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124 <valid><add value="|" /></valid>
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125 </sanitizer>
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126 </param>
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127 </when>
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128 <when value="dataset">
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129 <param name="id_spec" type="data" format="txt"
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130 label="Select a dataset with image IDs (one per line)" />
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131 </when>
10
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132 <when value="omeroDatasetID">
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133 <param name="id_dataset_omero" type="integer" min = "0" value = "9059" label="Dataset ID"/>
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134 </when>
0
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135 </conditional>
11
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136
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137 <conditional name="image_region">
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138 <param name="original" type="select" label="Which images do you want to download?">
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139 <option value="TIFF" selected="true">Exported TIFF (single channel, single stack)</option>
13
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140 <option value="full">Whole TIFF (all channels, all frames, all stacks)</option>
11
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141 <option value="original">Original file (file uploaded to omero, only available for private instances)</option>
0
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142 </param>
11
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143 <when value="original"/>
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144 <when value="full"/>
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145 <when value="TIFF">
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146 <param name="channel" type="text"
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147 label="Name of the channel to download"
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148 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." />
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149 <param name="z_section" type="integer" value="0" min="0"
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150 label="z-plane of images to download" />
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151 <param name="frame" type="integer" value="0" min="0"
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152 label="Image frame to download" />
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153 <conditional name="clip_image">
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154 <param name="select" type="select"
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155 label="Limit the download to a selected region of the image?">
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156 <option value="">No, download the entire image plane</option>
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157 <option value="--rectangle">Specify a region using its upper-left corner</option>
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158 <option value="--center">Specify a width x height region around a central point</option>
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159 </param>
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160 <when value="" />
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161 <when value="--rectangle">
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162 <expand macro="region_spec" />
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163 </when>
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164 <when value="--center">
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165 <expand macro="region_spec" pos="center" />
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166 </when>
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167 </conditional>
0
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diff changeset
168 </when>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
169 </conditional>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
170 <param name="skip_failed" type="boolean" checked="false" truevalue="--skip-failed" falsevalue=""
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
171 label="Skip failed retrievals?"
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
172 help="By default the tool will fail with an error on the first non-retrievable image ID. Here, you can choose to skip non-retrievable image IDs and continue downloading the available ones instead. The error log will contain warnings about failed IDs in this case." />
4
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
173 <param name="download_tar" type="boolean" checked="true" truevalue="--download-tar" falsevalue=""
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
174 label="Download images in a tarball?"
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
175 help="By default, the tool will download a tarball containing individual images into your Galaxy history. This option is strongly recommended, especially for a large number of files. With this option set to No, you will download a collection of images, only suggested for a small number of files." >
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
176 </param>
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
177 </inputs>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
178 <outputs>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
179 <data name="out_log" format="txt" label="${tool.name} error log" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
180 <collection name="output_file" type="list">
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
181 <discover_datasets pattern="__name_and_ext__" directory="downloads" />
4
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
182 <filter>not download_tar</filter>
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
183 </collection>
4
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
184 <data name="output_tar" format="tar" from_work_dir="./downloads/images.tar" label ="Images tarball">
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
185 <filter>download_tar</filter>
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
186 </data>
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
187 </outputs>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
188 <tests>
13
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
189 <test expect_num_outputs="2">
7
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
190 <conditional name="omero_instance_type">
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
191 <param name="omero_instance" value="idr" />
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
192 </conditional>
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
193 <param name="source" value="dataset" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
194 <param name="id_spec" value="ids.txt" />
11
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
195 <conditional name="image_region">
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
196 <param name="original" value="TIFF"/>
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
197 <param name="channel" value="PCNT" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
198 <conditional name="clip_image">
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
199 <param name="select" value="--rectangle" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
200 <param name="x_coord" value="3" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
201 <param name="y_coord" value="3" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
202 <param name="width" value="5" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
203 <param name="height" value="5" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
204 </conditional>
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
205 <param name="frame" value="0" />
7
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
206 </conditional>
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
207 <param name="download_tar" value="false" />
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
208 <output_collection name="output_file" type="list">
13
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
209 <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test0.tiff" compare="image_diff" />
7
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
210 </output_collection>
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
211 </test>
13
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
212 <test expect_num_outputs="2">
7
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
213 <conditional name="omero_instance_type">
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
214 <param name="omero_instance" value="idr" />
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
215 </conditional>
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
216 <param name="source" value="link" />
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
217 <param name="id_spec" value="1884807" />
11
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
218 <conditional name="image_region">
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
219 <param name="original" value="TIFF"/>
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
220 <param name="channel" value="PCNT" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
221 <conditional name="clip_image">
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
222 <param name="select" value="--rectangle" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
223 <param name="x_coord" value="3" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
224 <param name="y_coord" value="3" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
225 <param name="width" value="5" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
226 <param name="height" value="5" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
227 </conditional>
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
228 <param name="frame" value="2" />
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
229 </conditional>
4
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
230 <param name="download_tar" value="false" />
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
231 <output_collection name="output_file" type="list">
13
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
232 <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test1.tiff" compare="image_diff"/>
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
233 </output_collection>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
234 </test>
13
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
235 <test expect_num_outputs="2">
7
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
236 <conditional name="omero_instance_type">
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
237 <param name="omero_instance" value="idr" />
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
238 </conditional>
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
239 <param name="source" value="link" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
240 <param name="id_spec" value="1884807" />
11
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
241 <conditional name="image_region">
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
242 <param name="original" value="TIFF"/>
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
243 <param name="channel" value="PCNT" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
244 <conditional name="clip_image">
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
245 <param name="select" value="--center" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
246 <param name="x_coord" value="5" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
247 <param name="y_coord" value="5" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
248 <param name="width" value="5" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
249 <param name="height" value="5" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
250 </conditional>
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
251 <param name="frame" value="2" />
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
252 </conditional>
4
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
253 <param name="download_tar" value="false" />
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
254 <output_collection name="output_file" type="list">
13
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
255 <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" ftype="tiff" file="test2.tiff" compare="image_diff"/>
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
256 </output_collection>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
257 </test>
13
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
258 <test expect_num_outputs="2">
7
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
259 <conditional name="omero_instance_type">
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
260 <param name="omero_instance" value="idr" />
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
261 </conditional>
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
262 <param name="source" value="link" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
263 <param name="id_spec" value="https://idr.openmicroscopy.org/webclient/?show=image-9036708|image-9036710|image-9036711" />
11
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
264 <conditional name="image_region">
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
265 <param name="original" value="TIFF"/>
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
266 <param name="channel" value="Spo20(51-91)" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
267 <param name="z_section" value="4" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
268 <conditional name="clip_image">
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
269 <param name="select" value="" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
270 </conditional>
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
271 <param name="frame" value="20" />
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
272 </conditional>
4
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
273 <param name="download_tar" value="false" />
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
274 <output_collection name="output_file" type="list" count="3">
1
9340cbc7796c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit c496b34c7f6265cccd9326fd239542d9e625c1a4"
iuc
parents: 0
diff changeset
275 <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024">
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
276 <assert_contents>
13
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
277 <has_size size="2097286" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
278 <has_image_width width="1024" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
279 <has_image_height height="1024" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
280 <has_image_mean_intensity mean_intensity="320.868" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
281 <has_image_center_of_mass center_of_mass="541.664, 456.743" />
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
282 </assert_contents>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
283 </element>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
284 </output_collection>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
285 <output name="out_log">
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
286 <assert_contents>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
287 <has_text text="(ID: 9036710): Specified image plane (4) is out of bounds"/>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
288 <has_n_lines n="1"/>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
289 </assert_contents>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
290 </output>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
291 </test>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
292 <test expect_failure="true">
7
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
293 <conditional name="omero_instance_type">
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
294 <param name="omero_instance" value="idr" />
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
295 </conditional>
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
296 <!-- Test behavior with non-existing image-ID 9036708999 -->
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
297 <param name="source" value="link" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
298 <param name="id_spec" value="https://idr.openmicroscopy.org/webclient/?show=image-9036708999|image-9036710|image-9036711" />
11
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
299 <conditional name="image_region">
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
300 <param name="original" value="TIFF"/>
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
301 <param name="channel" value="Spo20(51-91)" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
302 <param name="z_section" value="4" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
303 <conditional name="clip_image">
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
304 <param name="select" value="" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
305 </conditional>
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
306 <param name="frame" value="20" />
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
307 </conditional>
4
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
308 <param name="download_tar" value="false" />
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
309 </test>
13
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
310 <test expect_num_outputs="2">
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
311 <!-- Repeat test with non-existing image-ID 9036708999,
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
312 but use skip-failed option -->
7
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
313 <conditional name="omero_instance_type">
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
314 <param name="omero_instance" value="idr" />
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
315 </conditional>
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
316 <param name="source" value="link" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
317 <param name="id_spec" value="https://idr.openmicroscopy.org/webclient/?show=image-9036708999|image-9036710|image-9036711" />
11
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
318 <conditional name="image_region">
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
319 <param name="original" value="TIFF"/>
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
320 <param name="channel" value="Spo20(51-91)" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
321 <param name="z_section" value="4" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
322 <conditional name="clip_image">
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
323 <param name="select" value="" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
324 </conditional>
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
325 <param name="frame" value="20" />
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
326 </conditional>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
327 <param name="skip_failed" value="true" />
4
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
328 <param name="download_tar" value="false" />
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
329 <output_collection name="output_file" type="list" count="2">
1
9340cbc7796c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit c496b34c7f6265cccd9326fd239542d9e625c1a4"
iuc
parents: 0
diff changeset
330 <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024">
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
331 <assert_contents>
13
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
332 <has_size size="2097286" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
333 <has_image_width width="1024" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
334 <has_image_height height="1024" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
335 <has_image_mean_intensity mean_intensity="320.868" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
336 <has_image_center_of_mass center_of_mass="541.664, 456.743" />
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
337 </assert_contents>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
338 </element>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
339 </output_collection>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
340 <output name="out_log">
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
341 <assert_contents>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
342 <has_text text="9036708999: Unable to find an image with this ID in the database. Skipping download!" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
343 <has_text text="(ID: 9036710): Specified image plane (4) is out of bounds" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
344 <has_n_lines n="2"/>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
345 </assert_contents>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
346 </output>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
347 </test>
13
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
348 <test expect_num_outputs="2">
7
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
349 <conditional name="omero_instance_type">
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
350 <param name="omero_instance" value="idr" />
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
351 </conditional>
4
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
352 <!-- Test for download images in a tarball -->
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
353 <param name="source" value="dataset" />
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
354 <param name="id_spec" value="ids_tar.txt" />
11
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
355 <conditional name="image_region">
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
356 <param name="original" value="TIFF"/>
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
357 <param name="channel" value="Hoechst" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
358 <conditional name="clip_image">
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
359 <param name="select" value="--rectangle" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
360 <param name="x_coord" value="0" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
361 <param name="y_coord" value="0" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
362 <param name="width" value="671" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
363 <param name="height" value="511" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
364 </conditional>
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
365 <param name="frame" value="0" />
4
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
366 </conditional>
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
367 <output name="output_tar">
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
368 <assert_contents>
13
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
369 <has_size size="1382400" />
4
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
370 <has_archive_member path=".*/*__1828167__0__0__671__511.tiff" >
13
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
371 <has_size size="685896" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
372 <has_image_width width="671" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
373 <has_image_height height="511" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
374 <has_image_mean_intensity mean_intensity="388.711" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
375 <has_image_center_of_mass center_of_mass="354.627, 267" />
4
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
376 </has_archive_member>
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
377 <has_archive_member path=".*/*__1828658__0__0__671__511.tiff" >
13
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
378 <has_size size="685896" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
379 <has_image_width width="671" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
380 <has_image_height height="511" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
381 <has_image_mean_intensity mean_intensity="397.507" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
382 <has_image_center_of_mass center_of_mass="346.098, 250.652" />
4
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
383 </has_archive_member>
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
384 </assert_contents>
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
385 </output>
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
386 </test>
13
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
387 <test expect_num_outputs="2">
8
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
iuc
parents: 7
diff changeset
388 <conditional name="omero_instance_type">
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
iuc
parents: 7
diff changeset
389 <param name="omero_instance" value="priv" />
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
iuc
parents: 7
diff changeset
390 <param name="omero_host" value="idr.openmicroscopy.org" />
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
iuc
parents: 7
diff changeset
391 <param name="omero_secured" value="true" />
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
iuc
parents: 7
diff changeset
392 <param name="galaxy_test_param" value="true" />
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
iuc
parents: 7
diff changeset
393 </conditional>
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
iuc
parents: 7
diff changeset
394 <param name="source" value="dataset" />
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
iuc
parents: 7
diff changeset
395 <param name="id_spec" value="ids.txt" />
11
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
396 <conditional name="image_region">
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
397 <param name="original" value="TIFF"/>
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
398 <param name="channel" value="PCNT" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
399 <conditional name="clip_image">
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
400 <param name="select" value="--rectangle" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
401 <param name="x_coord" value="3" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
402 <param name="y_coord" value="3" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
403 <param name="width" value="5" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
404 <param name="height" value="5" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
405 </conditional>
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
406 <param name="frame" value="0" />
8
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
iuc
parents: 7
diff changeset
407 </conditional>
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
iuc
parents: 7
diff changeset
408 <param name="download_tar" value="false" />
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
iuc
parents: 7
diff changeset
409 <output_collection name="output_file" type="list">
13
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
410 <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" file="test0.tiff" compare="image_diff"/>
8
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
iuc
parents: 7
diff changeset
411 </output_collection>
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
iuc
parents: 7
diff changeset
412 </test>
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
iuc
parents: 7
diff changeset
413 <test expect_failure="true">
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
iuc
parents: 7
diff changeset
414 <conditional name="omero_instance_type">
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
iuc
parents: 7
diff changeset
415 <param name="omero_instance" value="priv" />
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
iuc
parents: 7
diff changeset
416 <param name="omero_host" value="idr.openmicroscopy.org" />
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
iuc
parents: 7
diff changeset
417 <param name="omero_secured" value="true" />
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
iuc
parents: 7
diff changeset
418 </conditional>
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
iuc
parents: 7
diff changeset
419 <param name="source" value="dataset" />
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
iuc
parents: 7
diff changeset
420 <param name="id_spec" value="ids.txt" />
11
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
421 <conditional name="image_region">
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
422 <param name="original" value="TIFF"/>
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
423 <param name="channel" value="PCNT" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
424 <conditional name="clip_image">
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
425 <param name="select" value="--rectangle" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
426 <param name="x_coord" value="3" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
427 <param name="y_coord" value="3" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
428 <param name="width" value="5" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
429 <param name="height" value="5" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
430 </conditional>
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
431 <param name="frame" value="0" />
8
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
iuc
parents: 7
diff changeset
432 </conditional>
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
iuc
parents: 7
diff changeset
433 <param name="download_tar" value="false" />
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
iuc
parents: 7
diff changeset
434 <assert_stderr>
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
iuc
parents: 7
diff changeset
435 <has_text text="OMERO connection credentials are empty. Set your credentials via: User -> Preferences -> Manage Information" />
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
iuc
parents: 7
diff changeset
436 </assert_stderr >
97f70f7ed077 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit e337464c8219abdb7e8664ba94cff46025070664"
iuc
parents: 7
diff changeset
437 </test>
13
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
438 <test expect_num_outputs="2">
10
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
iuc
parents: 9
diff changeset
439 <conditional name="omero_instance_type">
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
iuc
parents: 9
diff changeset
440 <param name="omero_instance" value="idr" />
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
iuc
parents: 9
diff changeset
441 </conditional>
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
iuc
parents: 9
diff changeset
442 <!-- Test for download all images from a dataset -->
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
iuc
parents: 9
diff changeset
443 <param name="source" value="omeroDatasetID" />
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
iuc
parents: 9
diff changeset
444 <param name="id_dataset_omero" value="9059" />
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
iuc
parents: 9
diff changeset
445 <param name="download_tar" value="false" />
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
iuc
parents: 9
diff changeset
446 <output_collection name="output_file" type="list" count="4">
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
iuc
parents: 9
diff changeset
447 <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D__9036711__0__0__1024__1024">
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
iuc
parents: 9
diff changeset
448 <assert_contents>
13
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
449 <has_size size="2097286" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
450 <has_image_width width="1024" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
451 <has_image_height height="1024" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
452 <has_image_mean_intensity mean_intensity="145.310" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
453 <has_image_center_of_mass center_of_mass="527.499, 480.704" />
10
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
iuc
parents: 9
diff changeset
454 </assert_contents>
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
iuc
parents: 9
diff changeset
455 </element>
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
iuc
parents: 9
diff changeset
456 <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_D3D__9036708__0__0__1024__1024">
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
iuc
parents: 9
diff changeset
457 <assert_contents>
13
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
458 <has_size size="2097286" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
459 <has_image_width width="1024" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
460 <has_image_height height="1024" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
461 <has_image_mean_intensity mean_intensity="147.025" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
462 <has_image_center_of_mass center_of_mass="528.977, 480.691" />
10
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
iuc
parents: 9
diff changeset
463 </assert_contents>
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
iuc
parents: 9
diff changeset
464 </element>
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
iuc
parents: 9
diff changeset
465 <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_D3D_zproj__9036710__0__0__1024__1024">
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
iuc
parents: 9
diff changeset
466 <assert_contents>
13
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
467 <has_size size="2097286" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
468 <has_image_width width="1024" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
469 <has_image_height height="1024" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
470 <has_image_mean_intensity mean_intensity="210.787" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
471 <has_image_center_of_mass center_of_mass="534.629, 473.267" />
10
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
iuc
parents: 9
diff changeset
472 </assert_contents>
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
iuc
parents: 9
diff changeset
473 </element>
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
iuc
parents: 9
diff changeset
474 <element name="171101_LeadingEdgeDeletionPSMMovies01_15_R3D_REF__9036709__0__0__1024__1024">
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
iuc
parents: 9
diff changeset
475 <assert_contents>
13
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
476 <has_size size="2097286" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
477 <has_image_width width="1024" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
478 <has_image_height height="1024" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
479 <has_image_mean_intensity mean_intensity="3816.051" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
480 <has_image_center_of_mass center_of_mass="512.274, 503.186" />
10
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
iuc
parents: 9
diff changeset
481 </assert_contents>
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
iuc
parents: 9
diff changeset
482 </element>
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
iuc
parents: 9
diff changeset
483 </output_collection>
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
iuc
parents: 9
diff changeset
484 </test>
13
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
485 <test expect_num_outputs="2">
11
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
486 <conditional name="omero_instance_type">
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
487 <param name="omero_instance" value="idr" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
488 </conditional>
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
489 <!-- Test for download all original files from a dataset -->
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
490 <!-- Impossible in idr: -->
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
491 <param name="source" value="omeroDatasetID" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
492 <param name="id_dataset_omero" value="9059" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
493 <param name="skip_failed" value="true" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
494 <param name="download_tar" value="false" />
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
495 <conditional name="image_region">
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
496 <param name="original" value="original"/>
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
497 </conditional>
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
498 <output_collection name="output_file" type="list" count="0">
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
499 </output_collection>
cbd605a24336 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit b68715960d1107593db13dd9e1dbd8d4b905cc6f"
iuc
parents: 10
diff changeset
500 </test>
13
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
501 <test expect_num_outputs="2">
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
502 <conditional name="omero_instance_type">
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
503 <param name="omero_instance" value="idr" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
504 </conditional>
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
505 <param name="source" value="link" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
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diff changeset
506 <param name="id_spec" value="1229801" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
507 <param name="download_tar" value="false" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
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diff changeset
508 <conditional name="image_region">
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
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parents: 12
diff changeset
509 <param name="original" value="full"/>
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
510 </conditional>
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
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diff changeset
511 <output_collection name="output_file" type="list" count="1">
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
512 <element name="JL_120731_S6A_[Well_A-1;_Field_#1]__1229801__full">
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
513 <assert_contents>
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
514 <has_size size="91592058" />
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
515 </assert_contents>
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
516 </element>
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
517 </output_collection>
f92941d1a85e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit a9a143bae95eb6c553fd3d5955c2adb34352480f
iuc
parents: 12
diff changeset
518 </test>
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
519 </tests>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
520 <help><![CDATA[
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
521 Download image data from the IDR_ (Image Data Resource) - a public repository
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
522 of reference image datasets from published scientific studies.
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
523
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
524 .. _IDR: https://idr.openmicroscopy.org/about/
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
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diff changeset
525
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
526 -----
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
527
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
528 .. class:: infomark
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
529
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
530 **Input**
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
531
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
532 A set of image IDs as can be obtained from the IDR webclient_ like this:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
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diff changeset
533
3
381f248febba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 0ae8913ec1c14caedc9836d4889650ea836a1d70"
iuc
parents: 2
diff changeset
534 1. Select the wells you want to download in the thumbnails.
381f248febba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 0ae8913ec1c14caedc9836d4889650ea836a1d70"
iuc
parents: 2
diff changeset
535
381f248febba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 0ae8913ec1c14caedc9836d4889650ea836a1d70"
iuc
parents: 2
diff changeset
536 2. Select at the bottom the images in those wells that you want to download (one well might contain several images).
381f248febba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 0ae8913ec1c14caedc9836d4889650ea836a1d70"
iuc
parents: 2
diff changeset
537
381f248febba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 0ae8913ec1c14caedc9836d4889650ea836a1d70"
iuc
parents: 2
diff changeset
538 3. Click on the 'Link' button on the top right of the page and copy the provided URL.
381f248febba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 0ae8913ec1c14caedc9836d4889650ea836a1d70"
iuc
parents: 2
diff changeset
539
381f248febba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 0ae8913ec1c14caedc9836d4889650ea836a1d70"
iuc
parents: 2
diff changeset
540 4. Paste the URL into the input field of this tool, for example:
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
541
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
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diff changeset
542 https://idr.openmicroscopy.org/webclient/?show=image-9036708|image-9036710|image-9036711
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
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diff changeset
543
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
544 Alternatively, you can simply provide a list of known image IDs in the text
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
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diff changeset
545 input field (comma or '|'-separated ), or as an input file (each ID on a
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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diff changeset
546 separate line).
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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diff changeset
547
10
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
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diff changeset
548 Finally, if you want to download all images of a single dataset. Specify the id as
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
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parents: 9
diff changeset
549 All images from a single Dataset ID.
4aed70472589 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bb22e94226d3bcf241a6fe27e426b541a36a0815"
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parents: 9
diff changeset
550
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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parents:
diff changeset
551 Most images in the IDR have more than two dimensions. Thus, there are
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
552 parameters available which allow you to select a particular recording channel,
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
553 z-plane or time frame to download.
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
554 You can also select a region which will be used to crop the images, rather
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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parents:
diff changeset
555 than downloading the entire file.
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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parents:
diff changeset
556
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
557 .. _webclient: https://idr.openmicroscopy.org/
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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parents:
diff changeset
558
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
559
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
560 -----
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
561
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
562 .. class:: infomark
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
563
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
564 **Output**
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
565
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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diff changeset
566 Downloaded images will be saved in TIFF format. If you selected multiple image
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
567 IDs to download, these will be saved as elements of a collection.
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
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diff changeset
568
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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diff changeset
569 The accompanying error log dataset may hold valuable information about requests
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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diff changeset
570 that could not be fulfilled exactly as specified, or that were found to be
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
571 ambiguous.
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
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diff changeset
572 ]]></help>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
573 <citations>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
574 <citation type="doi">10.1038/nmeth.4326</citation>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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diff changeset
575 </citations>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
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diff changeset
576 </tool>