Mercurial > repos > iuc > ega_download_client

annotate pyega3.xml @ 2:e82175804eb1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit eb28ccaa03633b3500b38e2eb304c55e1682c489
author iuc
date Tue, 14 Jun 2022 17:06:07 +0000
parents 1162bfd9f782
children 8bbe09a52904
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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e82175804eb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit eb28ccaa03633b3500b38e2eb304c55e1682c489
iuc
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1 <tool id="pyega3" name="EGA Download Client" version="@TOOL_VERSION@+galaxy1" profile="21.01" >
0
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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2 <macros>
1
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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3 <token name="@TOOL_VERSION@">4.0.0</token>
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caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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4 </macros>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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5 <requirements>
1
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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6 <requirement type="package" version="@TOOL_VERSION@">pyega3</requirement>
0
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"
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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"
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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"
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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"
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12 #end if
caf213d51d6c "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" &&
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"
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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"
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20 files '$action.dataset_id'
1
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21 &&
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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22
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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23 ## create file header
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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24 echo -e 'File ID\tStatus\tBytes\tCheck sum\tFile name' > '$dataset_file_list' &&
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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25
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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26 ## remove timestamps and convert spaces to tabs
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
iuc
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27 grep EGAF pyega3_output.log | sed -e 's/^\[.*\]\s\+//g' | sed 's/\s\+/\t/g' >> '$dataset_file_list'
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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28
0
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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29 #elif $action.action_type == "download_file"
1
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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30 pyega3 -c \${PYEGA_CONNECTIONS:-30} -cf '$credentials'
0
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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31 fetch '$action.file_id'
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32 --max-retries 10
0
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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33 #if $action.range.reference_name
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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34 --reference-name '$action.range.reference_name'
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e82175804eb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit eb28ccaa03633b3500b38e2eb304c55e1682c489
iuc
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35 #if str($action.range.start)
0
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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36 --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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37 #end if
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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38 #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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39 --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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40 #end if
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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41 #end if
1
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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42 && mv ${action.file_id} downloads
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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43 && rm -f downloads/*.md5 ## checksum validation already performed by pyEGA, cleanup downloads folder
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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44
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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45 #elif $action.action_type == "download_files"
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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46 #set file_ids=[x.split('\t')[int(str($action.id_column))-1] for x in open(str($id_table)).readlines() if x.split('\t')[int(str($action.id_column))-1].startswith('EGAF') ]
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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47 mkdir downloads
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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48 #for f in $file_ids
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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49 &&
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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50 pyega3 -c \${PYEGA_CONNECTIONS:-30} -cf '$credentials'
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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51 fetch '$f'
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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52 --max-retries 10
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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53 #if $action.range.reference_name
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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54 --reference-name '$action.range.reference_name'
2
e82175804eb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit eb28ccaa03633b3500b38e2eb304c55e1682c489
iuc
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55 #if str($action.range.start)
1
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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56 --start $action.range.start
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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57 #end if
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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58 #if $action.range.end
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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59 --end $action.range.end
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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60 #end if
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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61 #end if
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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62 --output-dir downloads
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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63 #end for
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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64 && rm -f downloads/**/*.md5 ## checksum validation already performed by pyEGA, clean up downloads folder
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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65
0
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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66 #end if
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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67 ]]></command>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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68 <configfiles>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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69 <configfile name="credentials"><![CDATA[
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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70 #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"
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71 #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"
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72 #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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73 #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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74 #set $password = "egarocks"
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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75 #end if
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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76 {
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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77 "username": "$username",
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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78 "password": "$password"
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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79 }
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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80 ]]></configfile>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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81 </configfiles>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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82 <inputs>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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83 <conditional name="action">
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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84 <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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85 <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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86 <option value="list_dataset_files"> List files in a datasets </option>
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87 <option value="download_file"> Download a file </option>
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88 <option value="download_files"> Download multiple files (based on a file with IDs) </option>
0
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89 </param>
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90 <when value="list_dataset_files">
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91 <param name="dataset_id" type="text" optional="false" label="EGA Dataset Accession ID" help="Identifier starting with 'EGAD'. For example: EGAD00001003338">
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92 <validator type="regex" message="EGA dataset ID must be a string of numbers prefixed by 'EGAD'">EGAD[0-9]+</validator>
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93 </param>
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94 </when>
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95 <when value="list_datasets"/>
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96 <when value="download_file">
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97 <param name="file_id" type="text" optional="false" label="EGA File Accession Identifier" help="Identifier starting with 'EGAF'. For example: EGAF00001753735">
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98 <validator type="regex" message="EGA Accession ID must be a string of numbers prefixed by 'EGAD' (datasets) or 'EGAF' (files)">EGAF[0-9]+</validator>
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99 </param>
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100 <section name="range" title="Request a specific Genomic range?" expanded="false">
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101 <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." />
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102 <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"/>
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103 <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"/>
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104 </section>
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105 </when>
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106 <when value="download_files">
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107 <param name="id_table" type="data" format="tabular" label="Table with IDs to download" help="A tabular file where one column contains the set of file IDs. This will output a collection. Please select files that are all the same format (e.g. all BAM or all VCF)."/>
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108 <param name="id_column" type="data_column" data_ref="id_table" label="Column containing the file IDs" help="File Identifiers starting with 'EGAF'. For example: EGAF00001753735" />
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109 <section name="range" title="Request a specific Genomic range? (will be applied to ALL requested files)" expanded="false">
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110 <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." />
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111 <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"/>
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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112 <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"/>
0
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113 </section>
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114 </when>
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115 </conditional>
1
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116 <param name="output_log" type="boolean" checked="false" label="Output the log file?"/>
0
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117 </inputs>
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118 <outputs>
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119 <data name="authorized_datasets" format="txt" from_work_dir="pyega3_output.log" label="${tool.name}: authorized datasets">
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120 <filter> action['action_type'] == 'list_datasets' </filter>
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121 </data>
1
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122 <data name="dataset_file_list" format="tabular" label="${tool.name}: ${action.dataset_id} - file list">
0
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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123 <filter> action['action_type'] == 'list_dataset_files' </filter>
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124 </data>
1
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125 <data name="downloaded_file" auto_format="true" from_work_dir="downloads/*" label="${tool.name}: ${action.file_id} ${action.range.reference_name} ${action.range.start} ${action.range.end}">
0
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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126 <filter> action['action_type'] == 'download_file' </filter>
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127 </data>
1
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128 <data name="logfile" format="txt" from_work_dir="pyega3_output.log" label="${tool.name}: log">
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129 <filter> output_log </filter>
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130 </data>
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131 <collection name="downloaded_file_collection" type="list" label="${tool.name} on ${on_string}: Downloaded datasets">
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132 <filter> action['action_type'] == 'download_files' </filter>
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133 <discover_datasets pattern="__designation_and_ext__" recurse="true" directory="downloads" />
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134 </collection>
0
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135 </outputs>
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136 <tests>
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137 <test expect_num_outputs="1"><!-- list datasets with default credentials -->
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138 <param name="action_type" value="list_datasets"/>
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139 <output name="authorized_datasets" ftype="txt">
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140 <assert_contents>
1
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141 <has_text text="pyEGA3 - EGA python client version @TOOL_VERSION@"/>
0
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142 <has_text text="EGAD00001003338"/>
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143 </assert_contents>
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144 </output>
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145 </test>
1
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146 <test expect_num_outputs="2"><!-- list dataset files with default credentials, and request a log output file -->
0
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147 <param name="action_type" value="list_dataset_files"/>
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148 <param name="dataset_id" value="EGAD00001003338"/>
1
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149 <param name="output_log" value="true"/>
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150 <output name="dataset_file_list" file="filelist_EGAD00001003338.tabular"/>
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151 <output name="logfile" ftype="txt">
0
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152 <assert_contents>
1
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153 <has_text text="pyEGA3 - EGA python client version @TOOL_VERSION@"/>
0
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154 <has_line_matching expression="^\[.*\]\s+File ID\s+Status\s+Bytes\s+Check sum\s+File name$"/>
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155 <has_text text="EGAF00001753734"/>
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156 </assert_contents>
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157 </output>
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158 </test>
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159 <test expect_num_outputs="1"> <!-- download a single file -->
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160 <param name="action_type" value="download_file"/>
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161 <param name="file_id" value="EGAF00001775036"/>
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162 <output name="downloaded_file" md5="3b89b96387db5199fef6ba613f70e27c"/>
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163 </test>
1
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164 <test expect_num_outputs="1"> <!-- download a single file, with genomic range specified -->
0
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165 <param name="action_type" value="download_file"/>
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166 <param name="file_id" value="EGAF00001753756"/>
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167 <param name="reference_name" value="1"/>
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168 <param name="start" value="0"/>
0
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169 <param name="end" value="10000"/>
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170 <output name="downloaded_file" ftype="bam" md5="e576a38748feec45aa45191f6e902ce2"/>
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171 </test>
1
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172 <test expect_num_outputs="1"> <!-- download multiple files -->
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173 <param name="action_type" value="download_files"/>
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174 <param name="id_table" value="filelist.tabular"/>
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175 <param name="id_column" value="1"/>
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176 <output_collection name="downloaded_file_collection" type="list" count="2">
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177 <element name="ENCFF000VWO.bam" md5="b8ae14d5d1f717ab17d45e8fc36946a0" />
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178 <element name="ENCFF284YOU.bam" md5="3b89b96387db5199fef6ba613f70e27c" />
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179 </output_collection>
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180 </test>
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181 <test expect_num_outputs="1"> <!-- download multiple files, in combination with a genomic range -->
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182 <param name="action_type" value="download_files"/>
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183 <param name="id_table" value="filelist2.tabular"/>
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184 <param name="id_column" value="1"/>
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185 <param name="reference_name" value="1"/>
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186 <param name="start" value="0"/>
1
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187 <param name="end" value="10000"/>
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188 <output_collection name="downloaded_file_collection" count="2">
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189 <element name="NA19239_genomic_range_1_0_10000" md5="bcdcf18846233cbe5cc8afd95168552c" />
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190 <element name="NA19240_genomic_range_1_0_10000" md5="e576a38748feec45aa45191f6e902ce2" />
1
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191 </output_collection>
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192 </test>
0
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193 </tests>
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194 <help><![CDATA[
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195 The pyEGA3 download client is a python-based tool for viewing and downloading files from authorized EGA datasets.
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196
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197 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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198
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199 pyEGA3 uses the EGA Data API and has several key features:
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200
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201 - Files are transferred over secure https connections and received unencrypted, so no need for decryption after download.
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202 - Downloads resume from where they left off in the event that the connection is interrupted.
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203 - pyEGA3 supports file segmenting and parallelized download of segments, improving overall performance.
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204 - After download completes, file integrity is verified using checksums.
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205 - pyEGA3 implements the GA4GH-compliant htsget protocol for download of genomic ranges for data files with accompanying index files.
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206
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207 ]]></help>
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208 <citations>
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209 <citation type="doi">10.1038/ng.3312</citation>
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210 </citations>
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211 </tool>