annotate aarnet_filesender.xml @ 2:6d0c0961ae13 draft

planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
author galaxy-australia
date Mon, 21 Oct 2024 23:12:46 +0000
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6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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1 <tool id="aarnet_filesender" name="AARNet FileSender" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
galaxy-australia
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2 <description>transfer files with AARNet's FileSender Service</description>
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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3 <macros>
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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4 <import>macros.xml</import>
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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5 </macros>
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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6 <expand macro="requirements"/>
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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7 <expand macro="version_command"/>
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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8 <command detect_errors="exit_code"><![CDATA[
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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9 #if $test != "":
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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10 filesender -h &&
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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11 exit 0;
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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12 #end if
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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13
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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14 #set $apiuser = $__user__.extra_preferences.get('aarnet_filesender_account|username', "").strip()
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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15 #set $apikey = $__user__.extra_preferences.get('aarnet_filesender_account|apikey', "").strip()
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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16
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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17 #if $apiuser == "" or $apikey == "":
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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18 echo "ERROR: Please enter your FileSender Username in your user preferences under the AARNet FileSender Account Info section" >&2 &&
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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19 exit 1;
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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20 #end if
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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21
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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22 #if $to == "":
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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23 echo "WARNING: recipent email not set, setting to $__user_email__" &&
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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24 #set $to = $__user_email__
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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25 #end if
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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26
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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27 mkdir filestosend &&
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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28
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29 #for $file in $data
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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30 if [ -f "filestosend/${file.element_identifier}" ]; then
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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31 echo "ERROR: two datasets have the same name (${file.element_identifier})" &&
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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32 exit 1;
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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33 fi &&
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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34 ln -s "$file" "filestosend/${file.element_identifier}" &&
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35 #end for
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36
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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37 filesender -p -u '$apiuser' -a '$apikey' -b https://filesender.aarnet.edu.au/rest.php -f '$__user_email__' -r '$to' -s 'Data sent from Galaxy' filestosend >$output 2>&1
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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38 ]]></command>
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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39 <inputs>
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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40 <param name="data" type="data" format="data" multiple="true" optional="false" label="Datasets to be sent:"/>
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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41 <param name="to" type="text" optional="true" label="Email address of recipent:">
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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42 <sanitizer sanitize="False"/>
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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43 </param>
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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44 <param name="test" type="hidden" value=""/>
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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45 </inputs>
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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46 <outputs>
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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47 <data name="output" format="txt" hidden="false"/>
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48 </outputs>
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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49 <tests>
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50 <test expect_exit_code="1" expect_failure="true">
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51 <param name="data" value="summary_statistics.txt"/>
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52 <assert_stderr>
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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53 <has_text text="ERROR: Please enter your FileSender Username in your user preferences under the AARNet FileSender Account Info section"/>
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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54 </assert_stderr>
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55 </test>
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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56 <test>
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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57 <param name="data" value="summary_statistics.txt"/>
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58 <param name="test" value="true"/>
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59 <assert_stdout>
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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60 <has_text text="File Sender CLI client"/>
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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61 </assert_stdout>
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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62 </test>
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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63 </tests>
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64 <help>
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65 **What it does**
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66
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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67 Uses `AARNet’s FileSender service`_ to send dataset(s) from Galaxy. The
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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68 recipient will receive an email with a link to download the files.
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69
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70 **Who can use it**
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71
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72 AARNet FileSender is available to all institutions affiliated with the
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73 `Australian Access Federation (AAF)`_. You can use your institution
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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74 login details to access and use FileSender.
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75
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76 **How to connect your Galaxy account to FileSender**
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77
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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78 To send files from Galaxy you will need to connect your Galaxy account
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79 to FileSender. This is done by entering your FileSender API key into your
6d0c0961ae13 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/aarnet_filesender commit c8e1e0914854bf50287ea4b9ee86dfeb747a3342
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80 Galaxy user preferences.
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81
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82 1. Log in to FileSender, and copy your API key from the “API Secret” section on the FileSender “My
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83 Profile” page. See the `AARNet Knowledge Base`_ for more information.
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84 2. In Galaxy, add your API key to the “AARNet FileSender API Key” field
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85 in User &gt; Preferences &gt; Manage Information. Your AARNet FileSender
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86 Username is the email address you used to log in to FileSender.
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87
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88 .. _AARNet’s FileSender service: https://filesender.aarnet.edu.au
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89 .. _Australian Access Federation (AAF): https://aaf.edu.au/subscribers/
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90 .. _AARNet Knowledge Base: https://support.aarnet.edu.au/hc/en-us/articles/235972948-FileSender-API
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91 </help>
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92 <citations>
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93 <citation type="bibtex">
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94 @misc{FileSenderCLI_github,
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95 title={FileSenderCLI Github page},
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96 url = {https://github.com/madsi1m/FileSenderCLI},}
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97 </citation>
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98 </citations>
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99 </tool>