Mercurial > repos > iuc > idr_download_by_ids

annotate idr_download_by_ids.xml @ 7:f067504aa92a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
author iuc
date Thu, 05 Nov 2020 23:29:40 +0000
parents 5c743356df83
children 97f70f7ed077
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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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1 <?xml version="1.0"?>
7
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
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2 <tool id="idr_download_by_ids" name="IDR Download" version="0.43" profile="18.09">
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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3 <description>- download images from the Image Data Resource using image IDs</description>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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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"
iuc
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17 </macros>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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18 <requirements>
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f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
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19 <requirement type="package" version="5.7.1">python-omero</requirement>
2
17b1cd0f4812 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 7d7d50f41a9da71b0f45f8b710e52696689a8d85"
iuc
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20 <requirement type="package" version="0.4.2">pylibtiff</requirement>
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>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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22 <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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23
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
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24 #if $omero_instance_type.omero_instance == "priv":
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
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25 #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"
iuc
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26 #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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27
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
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28 #if $username == "" or $password =="":
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
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29 echo "OMERO connection credentials are empty. Set your credentials via: User -> Preferences -> Manage Information" &&
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
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30 exit 1
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
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31 #end if
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
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32 #end if
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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33
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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34 mkdir downloads && cd downloads &&
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
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35 #if str($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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36 python -c 'print("${image_ids.id_spec}".replace(",", "|").split("?show=")[-1].replace("|", "\n"))'
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
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37 ## https://idr.openmicroscopy.org/webclient/?show=image-3426274|image-3426275|image-3426276|image-3426277
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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38 #else:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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39 cat '${image_ids.id_spec}'
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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40 #end if
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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41 | python '$__tool_directory__/idr_download_by_ids.py'
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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42 #set $channel = str($channel).strip()
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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43 #if $channel:
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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44 -c '$channel'
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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45 #end if
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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46 -f $frame
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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47 -z $z_section
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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48 #if str($clip_image.select):
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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49 ${clip_image.select} ${clip_image.x_coord} ${clip_image.y_coord} ${clip_image.width} ${clip_image.height}
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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50 #end if
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51 $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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52 $download_tar
7
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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53 #if $omero_instance_type.omero_instance =='priv':
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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54 -h '$omero_host'
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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55 $omero_secured
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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56 -u '$username'
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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57 -p '$password'
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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58 #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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59 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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60 ]]></command>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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61 <inputs>
7
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62 <conditional name="omero_instance_type">
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63 <param name="omero_instance" type="select" label="Which OMERO instance to connect?"
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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64 help="By default, the tool will download a tarball containing individual images from IDR into your Galaxy history. If you
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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65 need to connect to your own instance, set your connection username and password from User->Preference->Manage Information" >
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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66 <option value="idr">IDR</option>
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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67 <option value="priv">other OMERO instance</option>
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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68 </param>
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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69 <when value="priv">
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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70 <param name="omero_host" type="text" label="OMERO host URL">
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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71 <validator type="regex" message="Enter a valid host location, for example, your.omero.server">
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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72 [.A-Za-z0-9_-]
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73 </validator>
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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74 </param>
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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75 <param name="omero_secured" type="boolean" label="Seured connection?" checked="true" truevalue="--omero-secured" falsevalue=""
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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76 help="Select Yes if your OMERO instance is running with SSL, otherwise select No">
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77 </param>
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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78 </when>
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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79 <when value="idr" />
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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80 </conditional>
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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81
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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82 <conditional name="image_ids">
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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83 <param name="source" type="select" label="How would you like to specify the IDs of images to download?">
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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84 <option value="link">As text (comma-separated list of IDs or a valid IDR link)</option>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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parents:
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85 <option value="dataset">As a dataset (one image ID per line)</option>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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parents:
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86 </param>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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parents:
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87 <when value="link">
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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88 <param name="id_spec" type="text"
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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89 label="Image IDs to download"
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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90 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.">
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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parents:
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91 <sanitizer>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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92 <valid><add value="|" /></valid>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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parents:
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93 </sanitizer>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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94 </param>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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95 </when>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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96 <when value="dataset">
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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97 <param name="id_spec" type="data" format="txt"
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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98 label="Select a dataset with image IDs (one per line)" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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parents:
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99 </when>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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100 </conditional>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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101 <param name="channel" type="text"
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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102 label="Name of the channel to download"
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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103 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." />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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104 <param name="z_section" 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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parents:
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105 label="z-plane of images to download" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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parents:
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106 <param name="frame" 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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parents:
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107 label="Image frame to download" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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parents:
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108 <conditional name="clip_image">
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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109 <param name="select" type="select"
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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110 label="Limit the download to a selected region 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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parents:
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111 <option value="">No, download the entire image plane</option>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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112 <option value="--rectangle">Specify a region using its upper-left corner</option>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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113 <option value="--center">Specify a width x height region around a central point</option>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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114 </param>
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115 <when value="" />
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116 <when value="--rectangle">
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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117 <expand macro="region_spec" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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118 </when>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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119 <when value="--center">
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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120 <expand macro="region_spec" pos="center" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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121 </when>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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122 </conditional>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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123 <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"
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124 label="Skip failed retrievals?"
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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125 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
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126 <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"
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127 label="Download images in a tarball?"
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
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128 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"
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129 </param>
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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130 </inputs>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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131 <outputs>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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132 <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"
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133 <collection name="output_file" type="list">
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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134 <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"
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135 <filter>not download_tar</filter>
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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136 </collection>
4
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
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137 <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"
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138 <filter>download_tar</filter>
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
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139 </data>
0
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140 </outputs>
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141 <tests>
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142 <test>
7
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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143 <conditional name="omero_instance_type">
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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144 <param name="omero_instance" value="idr" />
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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145 </conditional>
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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146 <param name="source" value="dataset" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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147 <param name="id_spec" value="ids.txt" />
7
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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148 <param name="channel" value="PCNT" />
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diff changeset
149 <conditional name="clip_image">
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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150 <param name="select" value="--rectangle" />
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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151 <param name="x_coord" value="3" />
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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152 <param name="y_coord" value="3" />
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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153 <param name="width" value="5" />
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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154 <param name="height" value="5" />
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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155 </conditional>
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156 <param name="frame" value="0" />
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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157 <param name="download_tar" value="false" />
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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158 <output_collection name="output_file" type="list">
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159 <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" file="test0.tiff"/>
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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160 </output_collection>
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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161 </test>
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162 <test>
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diff changeset
163 <conditional name="omero_instance_type">
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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164 <param name="omero_instance" value="idr" />
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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165 </conditional>
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
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166 <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
167 <param name="id_spec" value="1884807" />
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
168 <param name="channel" value="PCNT" />
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
169 <conditional name="clip_image">
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="select" value="--rectangle" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
171 <param name="x_coord" value="3" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
172 <param name="y_coord" value="3" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
173 <param name="width" value="5" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
174 <param name="height" value="5" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
175 </conditional>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
176 <param name="frame" value="2" />
4
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
177 <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
178 <output_collection name="output_file" type="list">
1
9340cbc7796c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit c496b34c7f6265cccd9326fd239542d9e625c1a4"
iuc
parents: 0
diff changeset
179 <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" file="test1.tiff"/>
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
180 </output_collection>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
181 </test>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
182 <test>
7
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
183 <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
184 <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
185 </conditional>
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
186 <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
187 <param name="id_spec" value="1884807" />
7
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
188 <param name="channel" value="PCNT" />
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
189 <conditional name="clip_image">
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
190 <param name="select" value="--center" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
191 <param name="x_coord" value="5" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
192 <param name="y_coord" value="5" />
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="width" value="5" />
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="height" value="5" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
195 </conditional>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
196 <param name="frame" value="2" />
4
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
197 <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
198 <output_collection name="output_file" type="list">
1
9340cbc7796c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit c496b34c7f6265cccd9326fd239542d9e625c1a4"
iuc
parents: 0
diff changeset
199 <element name="Centrin_PCNT_Cep215_20110506_Fri-1545_0_SIR_PRJ__1884807__3__3__5__5" file="test1.tiff"/>
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
200 </output_collection>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
201 </test>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
202 <test>
7
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
203 <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
204 <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
205 </conditional>
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
206 <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
207 <param name="id_spec" value="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
parents:
diff changeset
208 <param name="channel" value="Spo20(51-91)" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
209 <param name="z_section" value="4" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
210 <conditional name="clip_image">
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
211 <param name="select" value="" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
212 </conditional>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
213 <param name="frame" value="20" />
4
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
214 <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
215 <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
216 <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
217 <assert_contents>
2
17b1cd0f4812 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 7d7d50f41a9da71b0f45f8b710e52696689a8d85"
iuc
parents: 1
diff changeset
218 <has_size value="2097286" />
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
219 </assert_contents>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
220 </element>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
221 </output_collection>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
222 <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
223 <assert_contents>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
224 <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
225 <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
226 </assert_contents>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
227 </output>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
228 </test>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
229 <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
230 <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
231 <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
232 </conditional>
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
233 <!-- 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
234 <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
235 <param name="id_spec" value="https://idr.openmicroscopy.org/webclient/?show=image-9036708999|image-9036710|image-9036711" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
236 <param name="channel" value="Spo20(51-91)" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
237 <param name="z_section" value="4" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
238 <conditional name="clip_image">
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="select" value="" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
240 </conditional>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
241 <param name="frame" value="20" />
4
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
242 <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
243 </test>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
244 <test>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
245 <!-- 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
246 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
247 <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
248 <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
249 </conditional>
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
250 <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
251 <param name="id_spec" value="https://idr.openmicroscopy.org/webclient/?show=image-9036708999|image-9036710|image-9036711" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
252 <param name="channel" value="Spo20(51-91)" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
253 <param name="z_section" value="4" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
254 <conditional name="clip_image">
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
255 <param name="select" value="" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
256 </conditional>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
257 <param name="frame" value="20" />
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
258 <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
259 <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
260 <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
261 <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
262 <assert_contents>
2
17b1cd0f4812 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 7d7d50f41a9da71b0f45f8b710e52696689a8d85"
iuc
parents: 1
diff changeset
263 <has_size value="2097286" />
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
264 </assert_contents>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
265 </element>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
266 </output_collection>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
267 <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
268 <assert_contents>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
269 <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
270 <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
271 <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
272 </assert_contents>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
273 </output>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
274 </test>
4
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
275 <test>
7
f067504aa92a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 6b9df5f3cf2518e48eced93a2904a89776bde02d"
iuc
parents: 6
diff changeset
276 <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
277 <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
278 </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
279 <!-- 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
280 <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
281 <param name="id_spec" value="ids_tar.txt" />
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
282 <param name="channel" value="Hoechst" />
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
283 <conditional name="clip_image">
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
284 <param name="select" value="--rectangle" />
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
285 <param name="x_coord" value="0" />
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
286 <param name="y_coord" value="0" />
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
287 <param name="width" value="671" />
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
288 <param name="height" value="511" />
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
289 </conditional>
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
290 <param name="frame" value="0" />
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
291 <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
292 <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
293 <has_size value="1382400" />
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
294 <has_archive_member path=".*/*__1828167__0__0__671__511.tiff" >
6
5c743356df83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bf331f8e60e7bc1daf1cd71d2068062d925e7ffa"
iuc
parents: 5
diff changeset
295 <has_size value="685896" />
4
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
296 </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
297 <has_archive_member path=".*/*__1828658__0__0__671__511.tiff" >
6
5c743356df83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit bf331f8e60e7bc1daf1cd71d2068062d925e7ffa"
iuc
parents: 5
diff changeset
298 <has_size value="685896" />
4
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
299 </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
300 </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
301 </output>
11036f6197d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 3c3f1023af1edb4c63f59f4311cc078d9e88923f"
iuc
parents: 3
diff changeset
302 </test>
0
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
303 </tests>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
304 <help><![CDATA[
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
305 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
306 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
307
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
308 .. _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
parents:
diff changeset
309
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
310 -----
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
311
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
312 .. class:: infomark
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
313
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
314 **Input**
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
315
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
316 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"
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parents:
diff changeset
317
3
381f248febba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 0ae8913ec1c14caedc9836d4889650ea836a1d70"
iuc
parents: 2
diff changeset
318 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
319
381f248febba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 0ae8913ec1c14caedc9836d4889650ea836a1d70"
iuc
parents: 2
diff changeset
320 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
321
381f248febba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 0ae8913ec1c14caedc9836d4889650ea836a1d70"
iuc
parents: 2
diff changeset
322 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
323
381f248febba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 0ae8913ec1c14caedc9836d4889650ea836a1d70"
iuc
parents: 2
diff changeset
324 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
325
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
326 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
parents:
diff changeset
327
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
328 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
parents:
diff changeset
329 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"
iuc
parents:
diff changeset
330 separate line).
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
331
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
iuc
parents:
diff changeset
332 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
333 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
334 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:
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335 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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336 than downloading the entire file.
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337
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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338 .. _webclient: https://idr.openmicroscopy.org/
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339
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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340
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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341 -----
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342
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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343 .. class:: infomark
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344
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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345 **Output**
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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346
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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347 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"
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348 IDs to download, these will be saved as elements of a collection.
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349
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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350 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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351 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"
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352 ambiguous.
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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353 ]]></help>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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354 <citations>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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355 <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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356 </citations>
57aa9597cd31 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download commit 253efabdfea3a1fecc4c0f2c54c0e97a7d7960ab"
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357 </tool>