annotate pyega3.xml @ 7:7d87a9d58aa1 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 9b235992a96145b852de7a6b59bac3a33dcbbcc8
author iuc
date Tue, 03 Oct 2023 09:59:17 +0000
parents 6cb20e130473
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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8bbe09a52904 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit c472a64dc5e68fb058b71e7404f180847ba9f6d4
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1 <tool id="pyega3" name="EGA Download Client" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.01" >
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2 <macros>
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f9db47f68e5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 428637d89592a970388339a4ab68db9df8d68cdc
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3 <token name="@TOOL_VERSION@">5.0.2</token>
f9db47f68e5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 428637d89592a970388339a4ab68db9df8d68cdc
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4 <token name="@VERSION_SUFFIX@">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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5 </macros>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">pyega3</requirement>
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8 </requirements>
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8bbe09a52904 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit c472a64dc5e68fb058b71e7404f180847ba9f6d4
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9 <version_command><![CDATA[
8bbe09a52904 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit c472a64dc5e68fb058b71e7404f180847ba9f6d4
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10 pyega3 -v |& grep version | cut -d" " -f 10
8bbe09a52904 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit c472a64dc5e68fb058b71e7404f180847ba9f6d4
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11 ]]></version_command>
8bbe09a52904 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit c472a64dc5e68fb058b71e7404f180847ba9f6d4
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12 <command detect_errors="exit_code"><![CDATA[
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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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13 #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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14 #if $username == "":
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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15 #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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16 #end if
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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17 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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18
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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19 #if $action.action_type == "list_datasets"
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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20 pyega3 -cf '$credentials'
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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21 datasets
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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22 #elif $action.action_type == "list_dataset_files"
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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23 pyega3 -cf '$credentials'
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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24 files '$action.dataset_id'
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25 &&
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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26
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27 ## create file header
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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28 echo -e 'File ID\tStatus\tBytes\tCheck sum\tFile name' > '$dataset_file_list' &&
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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29
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30 ## remove timestamps and convert spaces to tabs
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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31 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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32
0
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33 #elif $action.action_type == "download_file"
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34 pyega3 -c \${PYEGA_CONNECTIONS:-30} -cf '$credentials'
0
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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35 fetch '$action.file_id'
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36 --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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37 #if $action.range.reference_name
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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38 --reference-name '$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
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39 #if str($action.range.start)
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40 --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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41 #end if
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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42 #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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43 --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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44 #end if
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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45 #end if
1
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46 && 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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47 && 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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48
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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49 #elif $action.action_type == "download_files"
3
8bbe09a52904 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit c472a64dc5e68fb058b71e7404f180847ba9f6d4
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50 #import re
8bbe09a52904 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit c472a64dc5e68fb058b71e7404f180847ba9f6d4
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51 #set file_ids=[x.split('\t')[int(str($action.id_column))-1] for x in open(str($id_table)).readlines()]
1
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52 mkdir downloads
4
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53 #for f in $file_ids
3
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54 #if not f.startswith("EGAF")
8bbe09a52904 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit c472a64dc5e68fb058b71e7404f180847ba9f6d4
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55 && >&2 echo "Ignoring \"$f\": no EGA file ID"
8bbe09a52904 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit c472a64dc5e68fb058b71e7404f180847ba9f6d4
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56 #continue
8bbe09a52904 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit c472a64dc5e68fb058b71e7404f180847ba9f6d4
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57 #end if
8bbe09a52904 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit c472a64dc5e68fb058b71e7404f180847ba9f6d4
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58 &&
4
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59 echo 'Downloading $f'
1
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60 &&
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61 pyega3 -c \${PYEGA_CONNECTIONS:-30} -cf '$credentials'
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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62 fetch '$f'
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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63 --max-retries 10
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64 #if $action.range.reference_name
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65 --reference-name '$action.range.reference_name'
2
e82175804eb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit eb28ccaa03633b3500b38e2eb304c55e1682c489
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66 #if str($action.range.start)
1
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67 --start $action.range.start
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68 #end if
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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69 #if $action.range.end
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70 --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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71 #end if
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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72 #end if
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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73 --output-dir downloads
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74 #end for
4
9564758e8638 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit a7400d366495a3e2bd6e0cb120834a59327537ec
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75 && for vcf in \$(ls downloads/**/*vcf.gz); do mv "\${vcf}" "\${vcf:0:-6}vcf_bgzip"; done ## renaming vcf.gz files to vcf_bgzip to recognize format
1
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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76 && 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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77
0
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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78 #end if
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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79 ]]></command>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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80 <configfiles>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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81 <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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82 #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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83 #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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84 #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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85 #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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86 #set $password = "egarocks"
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87 #end if
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88 {
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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89 "username": "$username",
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90 "password": "$password"
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91 }
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92 ]]></configfile>
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93 </configfiles>
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94 <inputs>
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95 <conditional name="action">
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96 <param name="action_type" type="select" label="What would you like to do?">
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97 <option value="list_datasets"> List my authorized datasets </option>
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98 <option value="list_dataset_files"> List files in a datasets </option>
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99 <option value="download_file"> Download a file </option>
1
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100 <option value="download_files"> Download multiple files (based on a file with IDs) </option>
0
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101 </param>
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102 <when value="list_dataset_files">
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103 <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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104 <validator type="regex" message="EGA dataset ID must be a string of numbers prefixed by 'EGAD'">EGAD[0-9]+</validator>
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105 </param>
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106 </when>
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107 <when value="list_datasets"/>
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108 <when value="download_file">
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109 <param name="file_id" type="text" optional="false" label="EGA File Accession Identifier" help="Identifier starting with 'EGAF'. For example: EGAF00001753735">
3
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110 <validator type="regex" message="EGA Accession ID must be a string of numbers prefixed by 'EGAD' (datasets) or 'EGAF' (files)">EGA[DF][0-9]+</validator>
0
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111 </param>
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112 <section name="range" title="Request a specific Genomic range?" expanded="false">
1
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113 <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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114 <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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115 <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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116 </section>
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117 </when>
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118 <when value="download_files">
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119 <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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120 <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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121 <section name="range" title="Request a specific Genomic range? (will be applied to ALL requested files)" expanded="false">
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122 <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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123 <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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124 <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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125 </section>
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126 </when>
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127 </conditional>
1
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128 <param name="output_log" type="boolean" checked="false" label="Output the log file?"/>
0
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129 </inputs>
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130 <outputs>
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131 <data name="authorized_datasets" format="txt" from_work_dir="pyega3_output.log" label="${tool.name}: authorized datasets">
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132 <filter> action['action_type'] == 'list_datasets' </filter>
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133 </data>
1
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134 <data name="dataset_file_list" format="tabular" label="${tool.name}: ${action.dataset_id} - file list">
0
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135 <filter> action['action_type'] == 'list_dataset_files' </filter>
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136 </data>
1
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137 <data name="downloaded_file" auto_format="true" from_work_dir="downloads/*" label="${tool.name}: ${action.file_id} ${action.range.reference_name} ${action.range.start} ${action.range.end}">
0
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138 <filter> action['action_type'] == 'download_file' </filter>
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139 </data>
1
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140 <data name="logfile" format="txt" from_work_dir="pyega3_output.log" label="${tool.name}: log">
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141 <filter> output_log </filter>
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142 </data>
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143 <collection name="downloaded_file_collection" type="list" label="${tool.name} on ${on_string}: Downloaded datasets">
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144 <filter> action['action_type'] == 'download_files' </filter>
4
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145 <discover_datasets pattern="__name_and_ext__" recurse="true" directory="downloads" />
1
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146 </collection>
0
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147 </outputs>
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148 <tests>
3
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149 <!-- list datasets with default credentials -->
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150 <test expect_num_outputs="1">
0
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151 <param name="action_type" value="list_datasets"/>
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152 <output name="authorized_datasets" ftype="txt">
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153 <assert_contents>
1
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154 <has_text text="pyEGA3 - EGA python client version @TOOL_VERSION@"/>
0
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155 <has_text text="EGAD00001003338"/>
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156 </assert_contents>
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157 </output>
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158 </test>
3
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159 <!-- list dataset files with default credentials, and request a log output file -->
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160 <test expect_num_outputs="2">
0
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161 <param name="action_type" value="list_dataset_files"/>
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162 <param name="dataset_id" value="EGAD00001003338"/>
1
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163 <param name="output_log" value="true"/>
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164 <output name="dataset_file_list" file="filelist_EGAD00001003338.tabular"/>
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165 <output name="logfile" ftype="txt">
0
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166 <assert_contents>
1
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parents: 0
diff changeset
167 <has_text text="pyEGA3 - EGA python client version @TOOL_VERSION@"/>
0
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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168 <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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169 <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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170 </assert_contents>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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171 </output>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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172 </test>
3
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diff changeset
173 <!-- download a single file -->
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diff changeset
174 <test expect_num_outputs="1">
0
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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175 <param name="action_type" value="download_file"/>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
iuc
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diff changeset
176 <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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diff changeset
177 <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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178 </test>
4
9564758e8638 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit a7400d366495a3e2bd6e0cb120834a59327537ec
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diff changeset
179 <!-- download a single vcf.gz -->
9564758e8638 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit a7400d366495a3e2bd6e0cb120834a59327537ec
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diff changeset
180 <test expect_num_outputs="1">
9564758e8638 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit a7400d366495a3e2bd6e0cb120834a59327537ec
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diff changeset
181 <param name="action_type" value="download_file"/>
9564758e8638 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit a7400d366495a3e2bd6e0cb120834a59327537ec
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diff changeset
182 <param name="file_id" value="EGAF00007243775"/>
9564758e8638 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit a7400d366495a3e2bd6e0cb120834a59327537ec
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parents: 3
diff changeset
183 <output name="downloaded_file" md5="51cfb69bf3b9416ff425381a58c18a2b" ftype="vcf_bgzip" />
9564758e8638 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit a7400d366495a3e2bd6e0cb120834a59327537ec
iuc
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diff changeset
184 </test>
9564758e8638 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit a7400d366495a3e2bd6e0cb120834a59327537ec
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diff changeset
185 <!-- download a single bam, with genomic range specified -->
3
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parents: 2
diff changeset
186 <test expect_num_outputs="1">
0
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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187 <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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diff changeset
188 <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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diff changeset
189 <param name="reference_name" value="1"/>
2
e82175804eb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit eb28ccaa03633b3500b38e2eb304c55e1682c489
iuc
parents: 1
diff changeset
190 <param name="start" value="0"/>
0
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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diff changeset
191 <param name="end" value="10000"/>
5
f9db47f68e5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 428637d89592a970388339a4ab68db9df8d68cdc
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diff changeset
192 <output name="downloaded_file" md5="4b5344ad094c2bed7787430259205098"/>
0
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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193 </test>
3
8bbe09a52904 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit c472a64dc5e68fb058b71e7404f180847ba9f6d4
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diff changeset
194 <!-- download multiple files -->
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195 <test expect_num_outputs="1">
1
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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parents: 0
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196 <param name="action_type" value="download_files"/>
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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diff changeset
197 <param name="id_table" value="filelist.tabular"/>
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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198 <param name="id_column" value="1"/>
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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199 <output_collection name="downloaded_file_collection" type="list" count="2">
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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200 <element name="ENCFF000VWO.bam" md5="b8ae14d5d1f717ab17d45e8fc36946a0" />
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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201 <element name="ENCFF284YOU.bam" md5="3b89b96387db5199fef6ba613f70e27c" />
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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diff changeset
202 </output_collection>
3
8bbe09a52904 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit c472a64dc5e68fb058b71e7404f180847ba9f6d4
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diff changeset
203 <assert_stderr>
8bbe09a52904 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit c472a64dc5e68fb058b71e7404f180847ba9f6d4
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204 <has_text text="Ignoring &quot;File ID&quot;: no EGA file ID"/>
8bbe09a52904 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit c472a64dc5e68fb058b71e7404f180847ba9f6d4
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205 </assert_stderr>
1
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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parents: 0
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206 </test>
3
8bbe09a52904 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit c472a64dc5e68fb058b71e7404f180847ba9f6d4
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diff changeset
207 <!-- download multiple files, in combination with a genomic range -->
8bbe09a52904 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit c472a64dc5e68fb058b71e7404f180847ba9f6d4
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diff changeset
208 <test expect_num_outputs="1">
1
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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parents: 0
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209 <param name="action_type" value="download_files"/>
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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210 <param name="id_table" value="filelist2.tabular"/>
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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211 <param name="id_column" value="1"/>
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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212 <param name="reference_name" value="1"/>
2
e82175804eb1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit eb28ccaa03633b3500b38e2eb304c55e1682c489
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213 <param name="start" value="0"/>
1
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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214 <param name="end" value="10000"/>
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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diff changeset
215 <output_collection name="downloaded_file_collection" count="2">
5
f9db47f68e5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 428637d89592a970388339a4ab68db9df8d68cdc
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216 <element name="NA19239_genomic_range_1_0_10000" md5="497f443830a6a3ec2e5bb5a19c4db638" />
f9db47f68e5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 428637d89592a970388339a4ab68db9df8d68cdc
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217 <element name="NA19240_genomic_range_1_0_10000" md5="4b5344ad094c2bed7787430259205098" />
1
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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218 </output_collection>
3
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219 <assert_stderr>
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220 <has_text text="Ignoring &quot;File ID&quot;: no EGA file ID"/>
8bbe09a52904 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit c472a64dc5e68fb058b71e7404f180847ba9f6d4
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221 </assert_stderr>
8bbe09a52904 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit c472a64dc5e68fb058b71e7404f180847ba9f6d4
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222 </test>
8bbe09a52904 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit c472a64dc5e68fb058b71e7404f180847ba9f6d4
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223 <!-- download multiple vcf.gz files -->
8bbe09a52904 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit c472a64dc5e68fb058b71e7404f180847ba9f6d4
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224 <test expect_num_outputs="1">
8bbe09a52904 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit c472a64dc5e68fb058b71e7404f180847ba9f6d4
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225 <param name="action_type" value="download_files"/>
8bbe09a52904 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit c472a64dc5e68fb058b71e7404f180847ba9f6d4
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diff changeset
226 <param name="id_table" value="filelist3.tabular"/>
8bbe09a52904 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit c472a64dc5e68fb058b71e7404f180847ba9f6d4
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227 <param name="id_column" value="1"/>
8bbe09a52904 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit c472a64dc5e68fb058b71e7404f180847ba9f6d4
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228 <output_collection name="downloaded_file_collection" type="list" count="2">
4
9564758e8638 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit a7400d366495a3e2bd6e0cb120834a59327537ec
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229 <element name="HG00408.novoBreak__256r__4.100100-10100100__7.200100-9000100" md5="51cfb69bf3b9416ff425381a58c18a2b" ftype="vcf_bgzip" />
9564758e8638 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit a7400d366495a3e2bd6e0cb120834a59327537ec
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230 <element name="HG01890.HGSVC__145r__1.900100-10001000__18.2001000-90001000" md5="ebad4425191a89d3e970c02190a87175" ftype="vcf_bgzip" />
3
8bbe09a52904 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit c472a64dc5e68fb058b71e7404f180847ba9f6d4
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231 </output_collection>
1
1162bfd9f782 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit f91c99780efc91e89950ed9494ef9e6f83d198c7"
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232 </test>
0
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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233 </tests>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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234 <help><![CDATA[
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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235 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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236
6
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diff changeset
237 .. class:: Warning mark
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diff changeset
238
6cb20e130473 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3ac2b4221e3aa5de4cef9f453ac1a7425ce130c2
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diff changeset
239 Data is stored unencrypted on the user's Galaxy account. Confidential data from the EGA could be left unprotected when uploaded to a public Galaxy server.
7
7d87a9d58aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 9b235992a96145b852de7a6b59bac3a33dcbbcc8
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diff changeset
240 Make sure to read the EGA Data Access Agreement (DAA_) before uploading any data to Galaxy from the EGA.
7d87a9d58aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 9b235992a96145b852de7a6b59bac3a33dcbbcc8
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diff changeset
241 If this applies to you, we recommend you follow the GalaxySensitiveData-ELIXIR-IS_ page for updates on encrypted data at rest.
6
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diff changeset
242
0
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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243 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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244
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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diff changeset
245 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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246
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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247 - 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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248 - 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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249 - pyEGA3 supports file segmenting and parallelized download of segments, improving overall performance.
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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250 - 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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251 - pyEGA3 implements the GA4GH-compliant htsget protocol for download of genomic ranges for data files with accompanying index files.
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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252
7
7d87a9d58aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 9b235992a96145b852de7a6b59bac3a33dcbbcc8
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253 .. _DAA: https://ega-archive.org/files/Example_DAA.doc
7d87a9d58aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 9b235992a96145b852de7a6b59bac3a33dcbbcc8
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254 .. _GalaxySensitiveData-ELIXIR-IS: https://github.com/elixir-europe/GalaxySensitiveData-ELIXIR_IS
0
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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255 ]]></help>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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256 <citations>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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257 <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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258 </citations>
caf213d51d6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pyega3 commit 3da28c7772346e1872b6d768b904305be0c61db7"
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259 </tool>