Mercurial > repos > rhohensinner > galaxy_irods_interface

annotate tug_download.xml @ 3:d2be2eb8350f draft

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"planemo upload commit b2a00d9c24285fef0fb131d1832ecf4c337e5038-dirty"
author rhohensinner
date Mon, 19 Jul 2021 13:11:45 +0000
parents 0641ea2f75b1
children 84f685c067ad
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3
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1 <tool id="irods_download" name="iRODS Download" version="0.3" workflow_compatible="false">
2
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2 <description>Download your files from iRODS into 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 ## Set up iRODS params
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10 #import json
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11 #set params = {}
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12 #set params["irods_host"] = str($custom_host)
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13 #set params["irods_port"] = str($custom_port)
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14 #set params["irods_zone"] = str($custom_zone)
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15 ##set params["filepath"] = str($file_path)
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16 #set params["file_path"] = str($file_path)
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17 ## set up Galaxy params
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18 #set params["galaxy_user"] = str($__user_name__)
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19 #set params["job_id"] = str($output.creating_job.id)
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20 #set params["out_dir"] = str($output.files_path)
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21 #set params["out_file"] = str($output)
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22 #set params["galaxy_root"] = str($GALAXY_ROOT_DIR)
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23 #set params["galaxy_datatypes"] = str($GALAXY_DATATYPES_CONF_FILE)
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24 #set params["irods_user"] = str($user)
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25 #set params["irods_password"] = str($password)
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26 ##import os
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27 ##import glob
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28 ##set $test = glob.glob("os.getcwd()" + "/**/irods_galaxy_registry.xml", recursive=True)
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29 ##set params["reg_file"]
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30 #set params["tool_type"] = "down"
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31 #set $params=json.dumps($params)
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32 main.py '$params'
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33 </command>
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34
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35 <inputs>
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36 <param name="custom_host" type="text" value="data.cyverse.tugraz.at" label="iRODS Host:" />
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37 <param name="custom_port" type="text" value="1247" label="iRODS Port:" />
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38 <param name="custom_zone" type="text" value="TUG" label="iRODS Zone:" />
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39 <param name="file_path" type="text" value="E.g.: /ZONE/home/USER/my_data.txt" label="Path to iRODS File or Directory:" />
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40 <param name="user" type="text" value="" label="iRODS User:" />
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41 <param name="password" type="text" value="" label="iRODS Password:" />
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42 </inputs>
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43
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44 <outputs>
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45 <data name="output" label="${tool.name}: ${file_path}" auto_format="true" />
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46 </outputs>
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47
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48 <help>
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49 Download iRODS
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50
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51 </help>
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52 <citations>
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53 <citation type="bibtex">
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54 @misc{Download-iRODS,
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55 author = {Hohensinner, Richard},
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56 year = {2021},
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57 title = {iRODSTools},
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58 publisher = {GitLab},
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59 journal = {GitLab repository},
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60 url = {https://gitlab.tugraz.at/D463A320ED7901AB/galaxy_irods_tools},
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61 }
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62 </citation>
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63 </citations>
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64 </tool>