Mercurial > repos > iuc > ega_download_client

annotate pyega3.xml @ 0:feaf09d289f3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
author iuc
date Fri, 30 Oct 2020 22:19:30 +0000
parents
children 95e6ae085d2e
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0
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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1 <tool id="pyega3" name="EGA Download Client" version="@VERSION@+galaxy0" profile="19.09" >
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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2 <macros>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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3 <token name="@VERSION@">3.4.0</token>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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4 </macros>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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5 <requirements>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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6 <requirement type="package" version="@VERSION@">pyega3</requirement>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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7 </requirements>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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8 <command detect_errors="exit_code"><![CDATA[
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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9 #set $username = $__user__.extra_preferences.get('ega_account|username', "")
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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10 #if $username == "":
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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11 #set $username = "ega-test-data@ebi.ac.uk (default user)"
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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12 #end if
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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13 echo "Running as user: $username. Set your credentials via: User -> Preferences -> Manage Information" &&
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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14
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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15 #if $action.action_type == "list_datasets"
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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16 pyega3 -cf '$credentials'
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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17 datasets
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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18 #elif $action.action_type == "list_dataset_files"
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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19 pyega3 -cf '$credentials'
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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20 files '$action.dataset_id'
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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21 #elif $action.action_type == "download_file"
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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22 pyega3 -cf '$credentials'
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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23 fetch '$action.file_id'
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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24 #if $action.range.reference_name
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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25 --reference-name '$action.range.reference_name'
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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26 #if $action.range.start
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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27 --start $action.range.start
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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28 #end if
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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29 #if $action.range.end
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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30 --end $action.range.end
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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31 #end if
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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32 #end if
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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33 --saveto '$downloaded_file'
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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34 #end if
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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35 ]]></command>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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36 <configfiles>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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37 <configfile name="credentials"><![CDATA[
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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38 #set $password = $__user__.extra_preferences.get('ega_account|password', "")
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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39 #set $username = $__user__.extra_preferences.get('ega_account|username', "")
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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40 #if $username == "" or $password == "":
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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41 #set $username = "ega-test-data@ebi.ac.uk"
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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42 #set $password = "egarocks"
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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43 #end if
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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44 {
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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45 "username": "$username",
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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46 "password": "$password"
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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47 }
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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48 ]]></configfile>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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49 </configfiles>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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50 <inputs>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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51 <conditional name="action">
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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52 <param name="action_type" type="select" label="What would you like to do?">
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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53 <option value="list_datasets"> List my authorized datasets </option>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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54 <option value="list_dataset_files"> List files in a datasets </option>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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55 <option value="download_file"> Download a file </option>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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56 </param>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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57 <when value="list_dataset_files">
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58 <param name="dataset_id" type="text" optional="false" label="EGA Dataset Accession ID" help="Identifier starting with 'EGAD'. For example: EGAD00001003338">
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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59 <validator type="regex" message="EGA dataset ID must be a string of numbers prefixed by 'EGAD'">EGAD[0-9]+</validator>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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60 </param>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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61 </when>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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62 <when value="list_datasets"/>
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63 <when value="download_file">
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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64 <param name="file_id" type="text" optional="false" label="EGA File Accession Identifier" help="Identifier starting with 'EGAF'. For example: EGAF00001753735">
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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65 <validator type="regex" message="EGA Accession ID must be a string of numbers prefixed by 'EGAD' (datasets) or 'EGAF' (files)">EGAF[0-9]+</validator>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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66 </param>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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67 <section name="range" title="Request a specific Genomic range?" expanded="false">
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68 <param argument="--reference-name" type="text" optional="true" label="Reference Sequence Name" help="For example 'chr1', '1', or 'chrX'. If unspecified, all data is returned." />
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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69 <param argument="--start" type="integer" optional="true" min="0" label="Start Position" help="0-based, inclusive. Only used if a reference sequence name was specified"/>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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70 <param argument="--end" type="integer" optional="true" min="0" label="End Position" help="0-based, exclusive. Only used if a reference sequence name was specified"/>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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71 </section>
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72 </when>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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73 </conditional>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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74 </inputs>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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75 <outputs>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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76 <data name="authorized_datasets" format="txt" from_work_dir="pyega3_output.log" label="${tool.name}: authorized datasets">
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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77 <filter> action['action_type'] == 'list_datasets' </filter>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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78 </data>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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79 <data name="dataset_file_list" format="txt" from_work_dir="pyega3_output.log" label="${tool.name}: dataset file list">
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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80 <filter> action['action_type'] == 'list_dataset_files' </filter>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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81 </data>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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82 <data name="downloaded_file" auto_format="true" label="${tool.name}: ${action.file_id} ${action.range.reference_name} ${action.range.start} ${action.range.end}">
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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83 <filter> action['action_type'] == 'download_file' </filter>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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84 </data>
feaf09d289f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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85 </outputs>
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86 <tests>
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87 <test expect_num_outputs="1"><!-- list datasets with default credentials -->
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88 <param name="action_type" value="list_datasets"/>
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89 <output name="authorized_datasets" ftype="txt">
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90 <assert_contents>
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91 <has_text text="pyEGA3 - EGA python client version @VERSION@"/>
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92 <has_text text="EGAD00001003338"/>
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93 </assert_contents>
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94 </output>
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95 </test>
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96 <test expect_num_outputs="1"><!-- list dataset files with default credentials -->
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97 <param name="action_type" value="list_dataset_files"/>
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98 <param name="dataset_id" value="EGAD00001003338"/>
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99 <output name="dataset_file_list" ftype="txt">
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100 <assert_contents>
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101 <has_text text="pyEGA3 - EGA python client version @VERSION@"/>
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102 <has_line_matching expression="^\[.*\]\s+File ID\s+Status\s+Bytes\s+Check sum\s+File name$"/>
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103 <has_text text="EGAF00001753734"/>
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104 </assert_contents>
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105 </output>
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106 </test>
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107 <test expect_num_outputs="1"> <!-- download a single file -->
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108 <param name="action_type" value="download_file"/>
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109 <param name="file_id" value="EGAF00001775036"/>
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110 <output name="downloaded_file" md5="3b89b96387db5199fef6ba613f70e27c"/>
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111 </test>
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112 <test expect_num_outputs="1"> <!-- download a single file, with genomic range specified -->
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113 <param name="action_type" value="download_file"/>
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114 <param name="file_id" value="EGAF00001753756"/>
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115 <param name="reference_name" value="1"/>
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116 <param name="start" value="100"/>
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117 <param name="end" value="10000"/>
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118 <output name="downloaded_file" ftype="bam" md5="e576a38748feec45aa45191f6e902ce2"/>
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119 </test>
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120 </tests>
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121 <help><![CDATA[
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122 The pyEGA3 download client is a python-based tool for viewing and downloading files from authorized EGA datasets.
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123
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124 If you have an EGA account, you can set your EGA credentials in the user preferences menu of Galaxy. Otherwise, default EGA credentials with access to an example dataset will be used.
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125
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126 pyEGA3 uses the EGA Data API and has several key features:
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127
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128 - Files are transferred over secure https connections and received unencrypted, so no need for decryption after download.
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129 - Downloads resume from where they left off in the event that the connection is interrupted.
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130 - pyEGA3 supports file segmenting and parallelized download of segments, improving overall performance.
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131 - After download completes, file integrity is verified using checksums.
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132 - pyEGA3 implements the GA4GH-compliant htsget protocol for download of genomic ranges for data files with accompanying index files.
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133
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134 ]]></help>
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135 <citations>
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136 <citation type="doi">10.1038/ng.3312</citation>
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137 </citations>
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138 </tool>