annotate pyega3.xml @ 0:caf213d51d6c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
author iuc
date Fri, 30 Oct 2020 22:18:41 +0000
parents
children 1162bfd9f782
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caf213d51d6c "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" >
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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2 <macros>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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3 <token name="@VERSION@">3.4.0</token>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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4 </macros>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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5 <requirements>
caf213d51d6c "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>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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7 </requirements>
caf213d51d6c "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[
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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9 #set $username = $__user__.extra_preferences.get('ega_account|username', "")
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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10 #if $username == "":
caf213d51d6c "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)"
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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12 #end if
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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13 echo "Running as user: $username. Set your credentials via: User -> Preferences -> Manage Information" &&
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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14
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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15 #if $action.action_type == "list_datasets"
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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16 pyega3 -cf '$credentials'
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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17 datasets
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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18 #elif $action.action_type == "list_dataset_files"
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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19 pyega3 -cf '$credentials'
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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20 files '$action.dataset_id'
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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21 #elif $action.action_type == "download_file"
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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22 pyega3 -cf '$credentials'
caf213d51d6c "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'
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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24 #if $action.range.reference_name
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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25 --reference-name '$action.range.reference_name'
caf213d51d6c "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
caf213d51d6c "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
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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28 #end if
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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29 #if $action.range.end
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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30 --end $action.range.end
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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31 #end if
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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32 #end if
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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33 --saveto '$downloaded_file'
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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34 #end if
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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35 ]]></command>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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36 <configfiles>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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37 <configfile name="credentials"><![CDATA[
caf213d51d6c "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', "")
caf213d51d6c "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', "")
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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40 #if $username == "" or $password == "":
caf213d51d6c "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"
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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42 #set $password = "egarocks"
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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43 #end if
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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44 {
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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45 "username": "$username",
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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46 "password": "$password"
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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47 }
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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48 ]]></configfile>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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49 </configfiles>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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50 <inputs>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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51 <conditional name="action">
caf213d51d6c "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?">
caf213d51d6c "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>
caf213d51d6c "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>
caf213d51d6c "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>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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56 </param>
caf213d51d6c "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">
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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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">
caf213d51d6c "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>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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60 </param>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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61 </when>
caf213d51d6c "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"/>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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63 <when value="download_file">
caf213d51d6c "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">
caf213d51d6c "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>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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66 </param>
caf213d51d6c "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">
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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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." />
caf213d51d6c "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"/>
caf213d51d6c "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"/>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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71 </section>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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72 </when>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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73 </conditional>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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74 </inputs>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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75 <outputs>
caf213d51d6c "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">
caf213d51d6c "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>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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78 </data>
caf213d51d6c "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="${tool.name}: dataset file list">
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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80 <filter> action['action_type'] == 'list_dataset_files' </filter>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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81 </data>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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82 <data name="downloaded_file" auto_format="true" label="${tool.name}: ${action.file_id} ${action.range.reference_name} ${action.range.start} ${action.range.end}">
caf213d51d6c "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>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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84 </data>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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85 </outputs>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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86 <tests>
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87 <test expect_num_outputs="1"><!-- list datasets with default credentials -->
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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88 <param name="action_type" value="list_datasets"/>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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89 <output name="authorized_datasets" ftype="txt">
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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90 <assert_contents>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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91 <has_text text="pyEGA3 - EGA python client version @VERSION@"/>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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92 <has_text text="EGAD00001003338"/>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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93 </assert_contents>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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94 </output>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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95 </test>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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96 <test expect_num_outputs="1"><!-- list dataset files with default credentials -->
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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97 <param name="action_type" value="list_dataset_files"/>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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98 <param name="dataset_id" value="EGAD00001003338"/>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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99 <output name="dataset_file_list" ftype="txt">
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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100 <assert_contents>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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101 <has_text text="pyEGA3 - EGA python client version @VERSION@"/>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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102 <has_line_matching expression="^\[.*\]\s+File ID\s+Status\s+Bytes\s+Check sum\s+File name$"/>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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103 <has_text text="EGAF00001753734"/>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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104 </assert_contents>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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105 </output>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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106 </test>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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107 <test expect_num_outputs="1"> <!-- download a single file -->
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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108 <param name="action_type" value="download_file"/>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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109 <param name="file_id" value="EGAF00001775036"/>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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110 <output name="downloaded_file" md5="3b89b96387db5199fef6ba613f70e27c"/>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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111 </test>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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112 <test expect_num_outputs="1"> <!-- download a single file, with genomic range specified -->
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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113 <param name="action_type" value="download_file"/>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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114 <param name="file_id" value="EGAF00001753756"/>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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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"/>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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119 </test>
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120 </tests>
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121 <help><![CDATA[
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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122 The pyEGA3 download client is a python-based tool for viewing and downloading files from authorized EGA datasets.
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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123
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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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.
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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125
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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126 pyEGA3 uses the EGA Data API and has several key features:
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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127
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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128 - Files are transferred over secure https connections and received unencrypted, so no need for decryption after download.
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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129 - Downloads resume from where they left off in the event that the connection is interrupted.
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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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.
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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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
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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134 ]]></help>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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135 <citations>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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136 <citation type="doi">10.1038/ng.3312</citation>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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137 </citations>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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138 </tool>