Mercurial > repos > rhohensinner > galaxy_irods_interface

annotate tug_upload.xml @ 4:84f685c067ad draft default tip

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"planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
author rhohensinner
date Wed, 04 Aug 2021 12:01:55 +0000
parents d2be2eb8350f
children
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1 <tool id="irods_upload" name="iRODS Upload" version="0.4" workflow_compatible="false">
2
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2 <description>Upload your files to iRODS from Galaxy</description>
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3 <requirements>
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4 <requirement type="package" version="0.8.2">python-irodsclient</requirement>
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5 </requirements>
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6
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7 <command interpreter="python">
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8 ## using CHEETAH
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9 #import json
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10 #set params = {}
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11 #set params["irods_host"] = str($custom_host)
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12 #set params["irods_port"] = str($custom_port)
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13 #set params["irods_zone"] = str($custom_zone)
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14 ##if $irods_config.typeiRODS == "use_any_irods"
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15 ##set params["irods_host"] = str($irods_config.custom_host)
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16 ##set params["irods_port"] = str($irods_config.custom_port)
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17 ##set params["irods_zone"] = str($irods_config.custom_zone)
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18 ##end if
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19 ##if $irods_config.typeiRODS == "use_tug_irods"
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20 ##set params["irods_host"] = "data.cyverse.tugraz.at"
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21 ##set params["irods_port"] = "1247"
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22 ##set params["irods_zone"] = "TUG"
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23 ##end if
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24 ## set up Galaxy params
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25 #set params["galaxy_user"] = str($__user_name__)
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26 #set params["job_id"] = str($output.creating_job.id)
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27 #set params["out_dir"] = str($output.files_path)
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28 #set params["out_file"] = str($output)
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29 #set params["up_file"] = str($up_file.name)
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30 #set params["up_file_path"] = str($up_file)
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31 #set params["galaxy_root"] = str($GALAXY_ROOT_DIR)
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32 #set params["galaxy_datatypes"] = str($GALAXY_DATATYPES_CONF_FILE)
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33 #set params["tool_type"] = "up"
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34 #set params["irods_user"] = str($user)
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35 #set params["irods_password"] = str($password)
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36 #set $params=json.dumps($params)
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37 irods_main.py '$params'
2
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38 </command>
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39
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40 <inputs>
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41 <param name="custom_host" type="text" value="data.cyverse.tugraz.at" label="iRODS Host:" />
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42 <param name="custom_port" type="text" value="1247" label="iRODS Port:" />
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43 <param name="custom_zone" type="text" value="TUG" label="iRODS Zone:" />
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44 <param name="up_file" type="data" value="" label="Galaxy file to upload" />
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45 <param name="user" type="text" value="" label="iRODS User:" />
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46 <param name="password" type="text" value="" label="iRODS Password:" />
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47
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48 </inputs>
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49
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50 <outputs>
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51 <data name="output" auto_format="true" />
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52 </outputs>
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53
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54 <help>
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55 Upload RODS
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56
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57 </help>
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58 <citations>
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59 <citation type="bibtex">
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60 @misc{Upload-iRODS,
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61 author = {Hohensinner, Richard},
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62 year = {2021},
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63 title = {iRODSTools},
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64 publisher = {GitLab},
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65 journal = {GitLab repository},
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66 url = {https://gitlab.tugraz.at/D463A320ED7901AB/galaxy_irods_tools},
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67 }
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68 </citation>
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69 </citations>
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70 </tool>