Mercurial > repos > iuc > ena_upload
annotate ena_upload.xml @ 10:480d9e9d156b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
author | iuc |
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date | Fri, 27 Oct 2023 19:44:40 +0000 |
parents | a62c4a11a67d |
children | f803a68fc9e5 |
rev | line source |
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10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
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1 <tool id="ena_upload" name="ENA Upload tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05" license="MIT"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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2 <macros> |
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480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
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3 <token name="@TOOL_VERSION@">0.6.3</token> |
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
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4 <token name="@VERSION_SUFFIX@">0</token> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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5 <import>samples_macros.xml</import> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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6 </macros> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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7 <requirements> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
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8 <requirement type="package" version="@TOOL_VERSION@">ena-upload-cli</requirement> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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9 </requirements> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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10 <stdio> |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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11 <regex match="Oops" source="stderr" level="fatal"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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12 <regex match="different file names between command line and RUN table" source="stderr" level="fatal"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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13 </stdio> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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14 <command detect_errors="exit_code"><![CDATA[ |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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15 mkdir ./submission_files; |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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16 #set $studies_table_path = './submission_files/studies.tsv' |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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17 #set $samples_table_path = './submission_files/samples.tsv' |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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18 #set $experiments_table_path = './submission_files/experiments.tsv' |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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19 #set $runs_table_path = './submission_files/runs.tsv' |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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20 |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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21 #set $studies_table_path_updated = './submission_files/studies_updated.tsv' |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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22 #set $samples_table_path_updated = './submission_files/samples_updated.tsv' |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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23 #set $experiments_table_path_updated = './submission_files/experiments_updated.tsv' |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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24 #set $runs_table_path_updated = './submission_files/runs_updated.tsv' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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25 |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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26 #set working_dir = os.getcwd() |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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27 #if $action_options.input_format_conditional.input_format == "build_tables": |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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28 python '$__tool_directory__/extract_tables.py' --action $action_options.action --out_dir ./submission_files --studies $studies_json; |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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29 #end if |
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30 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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31 credentials_path='test_fake_path'; |
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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32 echo "username: test_user" > \$credentials_path; |
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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33 echo "password: test_password" >> \$credentials_path; |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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34 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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35 |
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36 #if $action_options.input_format_conditional.input_format == "build_tables": |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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37 cp $studies_table_path $studies_table_out && |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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38 cp $samples_table_path $samples_table_out && |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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39 cp $experiments_table_path $experiments_table_out && |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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40 cp $runs_table_path $runs_table_out && |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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41 #end if |
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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42 #if $action_options.input_format_conditional.input_format == "user_generated_tables": |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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43 ln -s '$action_options.input_format_conditional.experiments_users_table' $experiments_table_path && |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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44 ln -s '$action_options.input_format_conditional.studies_users_table' $studies_table_path && |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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45 ln -s '$action_options.input_format_conditional.runs_users_table' $runs_table_path && |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
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46 ln -s '$action_options.input_format_conditional.samples_users_table' $samples_table_path && |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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47 #end if |
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48 #if $action_options.input_format_conditional.input_format == "excel_tables": |
6f6537780379
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49 ln -s '$action_options.input_format_conditional.xlsx_file' ./xlsx_input.xlsx && |
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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50 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
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51 #if $action_options.test_submit_parameters.dry_run == "False" and $action_options.test_submit == "False": |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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52 webin_id=`grep 'username' $credentials`; |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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53 if [ "\$webin_id" = "" ]; then |
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54 ## No credentials in user defined preferences |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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55 ## Fallback to global defined credentials (if exist) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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56 #import os |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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57 #if os.path.isfile(os.environ.get('GALAXY_ENA_SECRETS', '')): |
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58 credentials_path=\${GALAXY_ENA_SECRETS}; |
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59 webin_id=`grep 'username' \$GALAXY_ENA_SECRETS`; |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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60 if [ "\$webin_id" = "" ]; then |
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61 echo "No global credentials defined. Check your GALAXY_ENA_SECRETS file or set your credentials via: User -> Preferences -> Manage Information"; |
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62 exit 1; |
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63 fi; |
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64 #else: |
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65 echo "No ENA credentials defined. Set your credentials via: User -> Preferences -> Manage Information"; |
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66 exit 1; |
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67 #end if |
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68 else |
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69 credentials_path='$credentials'; |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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70 fi; |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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71 #end if |
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72 |
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73 |
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74 ## create the list of files to upload and make the symlinks |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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75 #import re |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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76 #set $files_to_upload = list() |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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77 #if $action_options.input_format_conditional.input_format == "build_tables": |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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78 #for $study in $action_options.input_format_conditional.conditional_viral_metadata.rep_study: |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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79 #for $sample in $study.rep_sample: |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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80 #for $experiment in $sample.rep_experiment: |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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81 #for $run in $experiment.rep_runs: |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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82 #for $file in $run.upload_files: |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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83 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier) |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
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84 #if $action_options.input_format_conditional.add_extension == "True": |
4
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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85 #set $extension = '.fastq' |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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86 #else |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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87 #set $extension = '' |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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88 #end if |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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89 #if $file.is_of_type('fastq', 'fastqsanger'): |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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90 ## compression output is defined as safename_reads_file so no need to symlink |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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91 #set $safename_reads_file = $safename_reads_file + $extension + '.gz' |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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92 gzip -c '$file' > $safename_reads_file && |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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93 #else: |
10
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
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94 #if $action_options.input_format_conditional.add_extension == "True": |
4
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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95 #if $file.is_of_type('fastq.gz', 'fastqsanger.gz'): |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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96 #set $compression = '.gz' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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97 #elif $file.is_of_type('fastqsanger.bz2', 'fastq.bz2'): |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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98 #set $compression = '.bz2' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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99 #end if |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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100 #set $safename_reads_file = $safename_reads_file + $extension + $compression |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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101 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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102 ln -s '$file' $safename_reads_file && |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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103 #end if |
0
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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104 $files_to_upload.append(str($safename_reads_file)) |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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105 #end for |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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106 #end for |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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107 #end for |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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108 #end for |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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109 #end for |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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110 #else: |
1
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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111 #if $action_options.input_format_conditional.run_input_format_conditional.run_input_format == 'paired_list': |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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112 #for $pair in $action_options.input_format_conditional.run_input_format_conditional.paired_end_collection: |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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113 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $pair.name) |
4
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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114 ## Always need to add .fastq + compression suffix because the name is based on the pair name which has no extensions |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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115 #if $pair.forward.is_of_type('fastq', 'fastqsanger'): |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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116 ## compress the file, no need to create the link then |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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117 ## always add the compression suffix (.gz) |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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118 #set $safename_fwd_reads_file = $safename_reads_file + '_1' + 'fastq' + '.gz' |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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119 gzip -c '$file' > $safename_fwd_reads_file && |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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120 #else |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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121 #if $pair.forward.is_of_type('fastq.gz', 'fastqsanger.gz'): |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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122 #set $compression = '.gz' |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
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123 #elif $pair.forward.is_of_type('fastqsanger.bz2', 'fastq.bz2'): |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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124 #set $compression = '.bz2' |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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125 #end if |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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126 #set $safename_fwd_reads_file = $safename_reads_file + '_1' + '.fastq' + $compression |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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127 ln -s '$pair.forward' $safename_fwd_reads_file && |
1
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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128 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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129 |
4
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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130 #if $pair.reverse.is_of_type('fastq', 'fastqsanger'): |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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131 ## compress the file, no need to create the link then |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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132 #set $safename_reverse_reads_file = $safename_reads_file + '_1' + '.fastq' + '.gz' |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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133 gzip -c '$file' > $safename_rev_reads_file && |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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134 #else |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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135 #if $pair.reverse.is_of_type('fastqsanger.bz2', 'fastq.bz2'): |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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136 #set $compression = '.bz2' |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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137 #elif $pair.reverse.is_of_type('fastqsanger.gz', 'fastq.gz'): |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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138 #set $compression = '.gz' |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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139 #end if |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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140 #set $safename_rev_reads_file = $safename_reads_file + '_2' + '.fastq' + $compression |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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141 ln -s '$pair.reverse' $safename_rev_reads_file && |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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142 #end if |
1
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
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143 $files_to_upload.append(str($safename_fwd_reads_file)) |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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144 $files_to_upload.append(str($safename_rev_reads_file)) |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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145 #end for |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
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146 #end if |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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147 #if $action_options.input_format_conditional.run_input_format_conditional.run_input_format == 'multiple_selection_list': |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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148 #for $file in $action_options.input_format_conditional.run_input_format_conditional.data: |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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149 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier) |
4
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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150 #if $file.is_of_type('fastq', 'fastqsanger'): |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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151 ## always compress add the gz extension |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
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152 #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "True": |
7
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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153 #set $safename_reads_file = $safename_reads_file + '.fastq.gz' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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154 #else |
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iuc
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155 #set $safename_reads_file = $safename_reads_file + '.gz' |
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480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
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156 #end if |
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iuc
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157 gzip -c '$file' > $safename_reads_file && |
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158 #else |
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159 #if $action_options.input_format_conditional.run_input_format_conditional.add_extension == "True": |
4
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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160 #if $file.is_of_type('fastq.gz', 'fastqsanger.gz'): |
7
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
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161 #set $extension = '.fastq.gz' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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162 #elif $file.is_of_type('fastqsanger.bz2', 'fastq.bz2'): |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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163 #set $extension = '.fastq.bz2' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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164 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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165 #set $safename_reads_file = $safename_reads_file + $extension |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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166 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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167 ln -s '$file' $safename_reads_file && |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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168 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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169 $files_to_upload.append(str($safename_reads_file)) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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170 #end for |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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171 #end if |
0
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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172 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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173 |
4
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174 #if $action_options.action == "add": |
0
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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175 ena-upload-cli |
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176 --tool 'ena-upload-cli v@TOOL_VERSION@ @ Galaxy' |
0
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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177 --action '$action_options.action' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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178 --center '$action_options.center' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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179 --secret \${credentials_path} |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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180 --data |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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181 #for $dataset in $files_to_upload: |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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182 '$dataset' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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183 #end for |
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184 #if $action_options.test_submit_parameters.dry_run == "True": |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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185 --draft |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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186 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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187 #if $action_options.input_format_conditional.input_format != "excel_tables": |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
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188 --experiment '$experiments_table_path' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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189 --study '$studies_table_path' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
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190 --run '$runs_table_path' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
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191 --sample '$samples_table_path' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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192 #else |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
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193 --xlsx ./xlsx_input.xlsx |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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194 #end if |
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iuc
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195 --action add |
0
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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196 #if $action_options.input_format_conditional.input_format == "user_generated_tables": |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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197 --checklist $action_options.input_format_conditional.checklist_id |
0
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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198 #else: |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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199 #if $action_options.input_format_conditional.input_format == "build_tables": |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
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200 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "True": |
4
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
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201 --checklist ERC000033 |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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202 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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203 #else: |
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iuc
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204 --checklist $action_options.input_format_conditional.checklist_id |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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205 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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206 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
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207 #if $action_options.idempotent == "True": |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
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208 --auto_action |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
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209 #end if |
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210 #if $action_options.test_submit_parameters.submit_dev == "True": |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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211 -d |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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212 #end if |
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213 >> '$output'; |
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214 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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215 |
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216 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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217 |
4
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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218 #if $action_options.action == "modify": |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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219 ena-upload-cli |
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220 --tool 'ena-upload-cli v@TOOL_VERSION@ @ Galaxy' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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221 --action '$action_options.action' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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222 --center '$action_options.center' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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223 --secret \${credentials_path} |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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224 --data |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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225 #for $dataset in $files_to_upload: |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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226 '$dataset' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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227 #end for |
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228 #if $action_options.test_submit_parameters.dry_run == "True": |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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229 --draft |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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230 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
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231 #if $action_options.input_format_conditional.input_format != "excel_tables": |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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232 --experiment '$experiments_table_path' |
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233 --study '$studies_table_path' |
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234 --run '$runs_table_path' |
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235 --sample '$samples_table_path' |
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236 #else |
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237 --xlsx ./xlsx_input.xlsx |
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238 --auto_action |
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239 #end if |
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240 --action 'modify' |
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241 #if $action_options.input_format_conditional.input_format == "user_generated_tables": |
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242 --checklist $action_options.input_format_conditional.checklist_id |
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243 #else: |
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244 #if $action_options.input_format_conditional.input_format == "build_tables": |
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245 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "True": |
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246 --checklist ERC000033 |
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247 #end if |
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248 #else: |
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249 --checklist $action_options.input_format_conditional.checklist_id |
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250 #end if |
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251 #end if |
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252 >> '$output'; |
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253 #end if |
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254 |
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255 #if $action_options.test_submit_parameters.dry_run == "False": |
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256 echo -e 'center_name\t$action_options.center' >> '$output'; |
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257 echo -e 'action_option\t$action_options.action' >> '$output'; |
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258 #end if |
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259 |
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260 ## copy updated files |
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261 #if $action_options.input_format_conditional.input_format == "excel_tables": |
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262 ## for the excel input case, copy the upload-cli generated tables to the output files |
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263 ## this applies for both draft and real submissions |
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264 cp './ENA_template_experiment_updated.tsv' $experiments_table_out; |
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265 cp './ENA_template_sample_updated.tsv' $samples_table_out; |
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266 cp './ENA_template_study_updated.tsv' $studies_table_out; |
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267 cp './ENA_template_run_updated.tsv' $runs_table_out; |
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268 #else |
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269 cp $studies_table_path_updated $studies_table_out 2>/dev/null; |
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270 cp $samples_table_path_updated $samples_table_out 2>/dev/null; |
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271 cp $experiments_table_path_updated $experiments_table_out 2>/dev/null; |
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272 cp $runs_table_path_updated $runs_table_out 2>/dev/null; |
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273 #end if |
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274 |
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275 python '$__tool_directory__/dump_yaml.py' $studies_table_out $samples_table_out $experiments_table_out $runs_table_out >> $output; |
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276 ]]></command> |
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277 <configfiles> |
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278 <configfile name="credentials"><![CDATA[ |
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279 #set $webin_id = $__user__.extra_preferences.get('ena_webin_account|webin_id', "").strip() |
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280 #set $password = $__user__.extra_preferences.get('ena_webin_account|password', "").strip() |
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281 #if $webin_id != "": |
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282 username: "$webin_id" |
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283 password: "$password" |
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284 #end if |
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285 ]]></configfile> |
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286 <configfile name="studies_json"> |
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287 #import json |
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288 #import re |
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289 #if $action_options.input_format_conditional.input_format == "build_tables": |
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290 #set $files_to_upload = list() |
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291 #set $studies = list() |
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292 #for $study in $action_options.input_format_conditional.conditional_viral_metadata.rep_study: |
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293 #set samples = list() |
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294 #for $sample in $study.rep_sample: |
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295 #set experiments = list() |
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296 #for $experiment in $sample.rep_experiment: |
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297 #set runs = list() |
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298 #for $run in $experiment.rep_runs: |
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299 #set run_files = list() |
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300 #for $file in $run.upload_files: |
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301 #set $safename_reads_file = re.sub('[^\w\-_\.]', '_', $file.element_identifier) |
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302 $run_files.append(str($safename_reads_file)) |
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303 #end for |
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304 $runs.append((str($run.run_base_name),$run_files)) |
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305 #end for |
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306 |
0
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307 $experiments.append({'title':str($experiment.experiment_title),'experiment_design':str($experiment.experiment_design),'library_strategy':str($experiment.library_strategy),'library_source':str($experiment.library_source),'library_selection':str($experiment.library_selection),'library_layout':str($experiment.library_layout),'insert_size':str($experiment.insert_size),'library_construction_protocol':str($experiment.library_construction_protocol),'platform':str($experiment.platform),'instrument_model':str($experiment.instrument_model),'runs':$runs}) |
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308 #end for |
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309 #if $action_options.input_format_conditional.conditional_viral_metadata.viral_sample == "True": |
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310 $samples.append({'title':str($sample.sample_title),'description':str($sample.sample_description),'tax_name':str($sample.scientific_name),'tax_id':str($sample.tax_id),'collection_date':str($sample.collection_date),'geo_location':str($sample.geo_location_country),'host_common_name':str($sample.host_common_name),'host_subject_id':str($sample.host_subject_id),'host_health_state':str($sample.host_health_state),'host_sex':str($sample.host_sex),'host_scientific_name':str($sample.host_scientific_name),'collector_name':str($sample.collector_name),'collecting_institution':str($sample.collecting_institution),'isolate':str($sample.isolate),'experiments':$experiments}) |
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311 #else: |
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312 $samples.append({'title':str($sample.sample_title),'description':str($sample.sample_description),'tax_name':str($sample.scientific_name),'tax_id':str($sample.tax_id),'collection_date':str($sample.collection_date),'geo_location':str($sample.geo_location_country),'experiments':$experiments}) |
0
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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313 #end if |
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314 #end for |
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315 $studies.append({'title':str($study.study_title),'type':str($study.study_type),'abstract':str($study.study_abstract),'pubmed_id':str($study.study_pubmed_id),'samples':$samples}) |
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316 #end for |
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317 #echo $json.dumps($studies) |
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318 #end if |
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319 </configfile> |
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320 </configfiles> |
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321 <inputs> |
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322 <conditional name="action_options"> |
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323 <param name="action" type="select" label="Action to execute"> |
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324 <option value="add" selected="True">Add new data</option> |
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325 <option value="modify">Modify metadata</option> |
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326 </param> |
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327 <when value="add"> |
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328 <param type="boolean" name="idempotent" checked="False" label="Idempotent submissions: only add the elements that were not submitted before" help="NOTE: this feature is based on a beta parameter of the CLI that checks the remote ENA repository for entries using the alias. This remote detection can have False positives, i.e assumes that it's present in the repository but it's not"/> |
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329 <expand macro="test_submit_section"/> |
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330 <param name="test_submit" type="hidden" value="False" /> |
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331 <expand macro="table_inputs_macro" /> |
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332 </when> |
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333 <when value="modify"> |
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334 <expand macro="test_submit_section"/> |
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335 <param name="test_submit" type="hidden" value="False" /> |
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336 <expand macro="table_inputs_macro" /> |
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337 </when> |
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338 </conditional> |
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339 </inputs> |
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340 <outputs> |
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341 <data name="output" format="txt" label="ENA submission receipt"/> |
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342 <data name="studies_table_out" format="tabular" label="Studies table"> |
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343 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter> |
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344 </data> |
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345 <data name="samples_table_out" format="tabular" label="Samples table"> |
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346 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter> |
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347 </data> |
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348 <data name="experiments_table_out" format="tabular" label="Experiments table"> |
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349 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter> |
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350 </data> |
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351 <data name="runs_table_out" format="tabular" label="Runs table"> |
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352 <filter> action_options['input_format_conditional']['input_format'] == "build_tables" or action_options['input_format_conditional']['input_format'] == "excel_tables"</filter> |
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353 </data> |
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354 </outputs> |
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355 <tests> |
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356 <!--Test 1: excel input of VIRAL samples --> |
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357 <test expect_num_outputs="5"> |
0
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358 <conditional name="action_options"> |
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359 <param name="action" value="add"/> |
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360 <section name="test_submit_parameters"> |
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361 <param name="submit_dev" value="False" /> |
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362 <param name="dry_run" value="True" /> |
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363 </section> |
0
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364 <conditional name="input_format_conditional"> |
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365 <param name="input_format" value="excel_tables"/> |
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366 <param name="checklist_id" value="ERC000033"/> |
0
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367 <param name="xlsx_file" value="metadata_test_viral.xlsx"/> |
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368 <conditional name="run_input_format_conditional"> |
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369 <param name="add_extension" value="False"/> |
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370 <param name="run_input_format" value="multiple_selection_list"/> |
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371 <param name="data" value="C030_exp5_clean.fastq,C053_exp5_clean.fastq,C026_exp5_clean.fastq,C067_exp5_clean.fastq"/> |
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372 </conditional> |
0
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373 </conditional> |
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374 </conditional> |
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375 <param name="center" value="Some research center"/> |
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376 <output name="experiments_table_out"> |
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377 <assert_contents> |
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378 <has_n_lines n="5"/> |
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379 <has_n_columns n="17"/> |
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380 <has_line_matching expression="alias\ttitle\tstudy_alias\tsample_alias\tdesign_description\tlibrary_name\tlibrary_strategy\tlibrary_source\tlibrary_selection\tlibrary_layout\tinsert_size\tlibrary_construction_protocol\tplatform\tinstrument_model\taccession\tsubmission_date\tstatus"/> |
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381 <has_line_matching expression="e_(.*)_026\tNanopore sequencing\tSARS-CoV-2_genomes_01\ts_(.*)"/> |
0
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382 </assert_contents> |
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383 </output> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
384 <output name="studies_table_out"> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
385 <assert_contents> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
386 <has_n_lines n="2"/> |
7
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
387 <has_n_columns n="7"/> |
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
388 <has_line_matching expression="SARS-CoV-2_genomes_01\tWhole-genome sequencing of SARS-CoV-2 from Covid-19 patients\tWhole Genome Sequencing\tWhole-genome sequences of SARS-CoV-2 from oro-pharyngeal swabs obtained from Covid-19 patients(.*)"/> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
389 </assert_contents> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
390 </output> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
391 <output name="samples_table_out"> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
392 <assert_contents> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
393 <has_n_lines n="5"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
394 <has_n_columns n="18"/> |
2
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
395 </assert_contents> |
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
396 </output> |
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
397 <output name="runs_table_out"> |
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
398 <assert_contents> |
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
399 <has_n_lines n="5"/> |
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
400 <has_n_columns n="8"/> |
7
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
401 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tstatus\tfile_checksum"/> |
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
402 <has_line_matching expression="r_20201007_026\te_20201007_026\tC026_exp5_clean.fastq.gz\tFASTQ(.*)"/> |
2
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
403 </assert_contents> |
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
404 </output> |
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
405 </test> |
4
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
406 <!--Test 2: excel input of VIRAL samples with extended columns--> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
changeset
|
407 <test expect_num_outputs="5"> |
2
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
408 <conditional name="action_options"> |
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
409 <param name="action" value="add"/> |
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
410 <section name="test_submit_parameters"> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
changeset
|
411 <param name="submit_dev" value="False" /> |
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
changeset
|
412 <param name="dry_run" value="True" /> |
2
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
413 </section> |
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
414 <conditional name="input_format_conditional"> |
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
415 <param name="input_format" value="excel_tables"/> |
7
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
416 <param name="checklist_id" value="ERC000033"/> |
2
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
417 <param name="xlsx_file" value="metadata_test_viral_optional_columns.xlsx"/> |
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
418 <conditional name="run_input_format_conditional"> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
changeset
|
419 <param name="add_extension" value="False"/> |
2
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
420 <param name="run_input_format" value="multiple_selection_list"/> |
7
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
421 <param name="data" value="C030_exp5_clean.fastq,C053_exp5_clean.fastq,C026_exp5_clean.fastq,C067_exp5_clean.fastq"/> |
2
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
422 </conditional> |
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
423 </conditional> |
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
424 </conditional> |
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
425 <param name="center" value="Some research center"/> |
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
426 <output name="experiments_table_out"> |
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
427 <assert_contents> |
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
428 <has_n_lines n="5"/> |
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
429 <has_n_columns n="17"/> |
7
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
430 <has_line_matching expression="alias\ttitle\tstudy_alias\tsample_alias\tdesign_description\tlibrary_name\tlibrary_strategy\tlibrary_source\tlibrary_selection\tlibrary_layout\tinsert_size\tlibrary_construction_protocol\tplatform\tinstrument_model\taccession\tsubmission_date\tstatus"/> |
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
431 <has_line_matching expression="e_(.*)_026\tNanopore sequencing\tSARS-CoV-2_genomes_01\ts_(.*)"/> |
2
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
432 </assert_contents> |
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
433 </output> |
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
434 <output name="studies_table_out"> |
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
435 <assert_contents> |
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
436 <has_n_lines n="2"/> |
7
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
437 <has_n_columns n="7"/> |
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
438 <has_line_matching expression="alias\ttitle\tstudy_type\tstudy_abstract\taccession\tsubmission_date\tstatus"/> |
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
439 <has_line_matching expression="SARS-CoV-2_genomes_01\tWhole-genome sequencing of SARS-CoV-2 from Covid-19 patients\tWhole Genome Sequencing\tWhole-genome sequences of SARS-CoV-2 from oro-pharyngeal swabs obtained from Covid-19 patients(.*)"/> |
2
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
440 </assert_contents> |
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
441 </output> |
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
442 <output name="samples_table_out"> |
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
443 <assert_contents> |
9e2df763086c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 1eed23745846ce215e9bdc4a4934d6bc8f41b24e"
iuc
parents:
1
diff
changeset
|
444 <has_n_lines n="5"/> |
7
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
445 <has_n_columns n="43"/> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
446 </assert_contents> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
447 </output> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
448 <output name="runs_table_out"> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
449 <assert_contents> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
450 <has_n_lines n="5"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
451 <has_n_columns n="8"/> |
7
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
452 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tstatus\tfile_checksum"/> |
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
453 <has_line_matching expression="r_20201007_026\te_20201007_026\tC026_exp5_clean.fastq.gz\tFASTQ(.*)"/> |
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
454 </assert_contents> |
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
455 </output> |
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
456 <output name="output"> |
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
457 <assert_contents> |
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
458 <has_line_matching expression="YAML -------------"/> |
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
459 <has_line_matching expression="ENA_experiment:"/> |
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
460 <has_line_matching expression="ENA_sample:"/> |
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
461 <has_line_matching expression="ENA_study:"/> |
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
462 <has_line_matching expression="ENA_run:"/> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
463 </assert_contents> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
464 </output> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
465 </test> |
4
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
466 <!--Test 3: excel input of NON-VIRAL samples--> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
changeset
|
467 <test expect_num_outputs="5"> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
468 <conditional name="action_options"> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
469 <param name="action" value="add"/> |
1
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
0
diff
changeset
|
470 <section name="test_submit_parameters"> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
changeset
|
471 <param name="submit_dev" value="False" /> |
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
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diff
changeset
|
472 <param name="dry_run" value="True" /> |
1
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
0
diff
changeset
|
473 </section> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
474 <conditional name="input_format_conditional"> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
475 <param name="input_format" value="excel_tables"/> |
7
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
476 <param name="checklist_id" value="ERC000011"/> |
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
477 <param name="xlsx_file" value="metadata_test_nonviral_1_run.xlsx"/> |
1
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
0
diff
changeset
|
478 <conditional name="run_input_format_conditional"> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
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diff
changeset
|
479 <param name="add_extension" value="True"/> |
1
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
0
diff
changeset
|
480 <param name="run_input_format" value="multiple_selection_list"/> |
7
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
481 <param name="data" value="sample_no_extension"/> |
1
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
0
diff
changeset
|
482 </conditional> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
483 </conditional> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
484 </conditional> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
485 <param name="center" value="Some research center"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
486 <output name="experiments_table_out"> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
487 <assert_contents> |
7
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
488 <has_n_lines n="2"/> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
489 <has_n_columns n="17"/> |
7
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
490 <has_line_matching expression="alias\ttitle\tstudy_alias\tsample_alias\tdesign_description\tlibrary_name\tlibrary_strategy\tlibrary_source\tlibrary_selection\tlibrary_layout\tinsert_size\tlibrary_construction_protocol\tplatform\tinstrument_model\taccession\tsubmission_date\tstatus"/> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
491 </assert_contents> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
492 </output> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
493 <output name="studies_table_out"> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
494 <assert_contents> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
495 <has_n_lines n="2"/> |
7
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
496 <has_n_columns n="7"/> |
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
497 <has_line_matching expression="alias\ttitle\tstudy_type\tstudy_abstract\taccession\tsubmission_date\tstatus"/> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
498 </assert_contents> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
499 </output> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
500 <output name="samples_table_out"> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
501 <assert_contents> |
7
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
502 <has_n_lines n="2"/> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
changeset
|
503 <has_n_columns n="10"/> |
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
changeset
|
504 <has_line_matching expression="s_20201007_026\tC026\tSaccharomyces cerevisiae\tSample from beer\t2020-03-25\tAntarctica\t\t\tADDED\t"/> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
505 </assert_contents> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
506 </output> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
507 <output name="runs_table_out"> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
508 <assert_contents> |
7
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
509 <has_n_lines n="2"/> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
510 <has_n_columns n="8"/> |
7
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
511 <has_line_matching expression="alias\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tstatus\tfile_checksum"/> |
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
512 <has_line_matching expression="r_20201007_026\te_20201007_026\tsample_no_extension.fastq.gz\tFASTQ(.*)"/> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
513 </assert_contents> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
514 </output> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
515 </test> |
4
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
516 <!--Test 4: failure on excel input of NON-VIRAL samples with runs PAIRED collection --> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
changeset
|
517 <test expect_failure="True"> |
1
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
0
diff
changeset
|
518 <conditional name="action_options"> |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
0
diff
changeset
|
519 <param name="action" value="add"/> |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
0
diff
changeset
|
520 <section name="test_submit_parameters"> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
changeset
|
521 <param name="submit_dev" value="False" /> |
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
changeset
|
522 <param name="dry_run" value="False" /> |
1
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
0
diff
changeset
|
523 </section> |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
0
diff
changeset
|
524 <conditional name="input_format_conditional"> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
changeset
|
525 <param name="add_extension" value="True"/> |
1
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
0
diff
changeset
|
526 <param name="input_format" value="excel_tables"/> |
7
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
527 <param name="checklist_id" value="ERC000011"/> |
1
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
0
diff
changeset
|
528 <param name="xlsx_file" value="metadata_test_nonviral.xlsx"/> |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
0
diff
changeset
|
529 <conditional name="run_input_format_conditional"> |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
0
diff
changeset
|
530 <param name="run_input_format" value="paired_list"/> |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
0
diff
changeset
|
531 <param name="paired_end_collection"> |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
0
diff
changeset
|
532 <collection type="list:paired"> |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
0
diff
changeset
|
533 <element name="paired_run_name"> |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
0
diff
changeset
|
534 <collection type="paired"> |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
0
diff
changeset
|
535 <element name="forward" value="1.fastqsanger.gz" ftype="fastqsanger.gz" /> |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
0
diff
changeset
|
536 <element name="reverse" value="2.fastqsanger.gz" ftype="fastqsanger.gz" /> |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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537 </collection> |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
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|
538 </element> |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
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539 </collection> |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
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|
540 </param> |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
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changeset
|
541 </conditional> |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
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|
542 </conditional> |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
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|
543 </conditional> |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
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|
544 <param name="center" value="Some research center"/> |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
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|
545 <assert_command> |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
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changeset
|
546 <has_text_matching expression="ena-upload-cli"/> |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
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|
547 <has_text_matching expression="--data 'paired_run_name_1.fastq.gz' 'paired_run_name_2.fastq.gz'"/> |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
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|
548 <has_text_matching expression="--action 'add' --center 'Some research center'"/> |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
0
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|
549 </assert_command> |
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
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|
550 </test> |
8
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents:
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diff
changeset
|
551 <!--Test 4b: failure on excel input of NON-VIRAL samples with runs PAIRED collection + Idempotent submission --> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
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552 <test expect_failure="True"> |
8
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents:
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diff
changeset
|
553 <conditional name="action_options"> |
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents:
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|
554 <param name="action" value="add"/> |
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents:
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diff
changeset
|
555 <section name="test_submit_parameters"> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
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|
556 <param name="submit_dev" value="False" /> |
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
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557 <param name="dry_run" value="False" /> |
8
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents:
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diff
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|
558 </section> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
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|
559 <param name="idempotent" value="True"/> |
8
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents:
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changeset
|
560 <conditional name="input_format_conditional"> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
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|
561 <param name="add_extension" value="True"/> |
8
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents:
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diff
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|
562 <param name="input_format" value="excel_tables"/> |
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
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|
563 <param name="checklist_id" value="ERC000011"/> |
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents:
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|
564 <param name="xlsx_file" value="metadata_test_nonviral.xlsx"/> |
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents:
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changeset
|
565 <conditional name="run_input_format_conditional"> |
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents:
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diff
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|
566 <param name="run_input_format" value="paired_list"/> |
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents:
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|
567 <param name="paired_end_collection"> |
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents:
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diff
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|
568 <collection type="list:paired"> |
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents:
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diff
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|
569 <element name="paired_run_name"> |
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents:
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diff
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|
570 <collection type="paired"> |
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents:
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diff
changeset
|
571 <element name="forward" value="1.fastqsanger.gz" ftype="fastqsanger.gz" /> |
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents:
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diff
changeset
|
572 <element name="reverse" value="2.fastqsanger.gz" ftype="fastqsanger.gz" /> |
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents:
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diff
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573 </collection> |
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents:
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|
574 </element> |
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents:
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575 </collection> |
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
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576 </param> |
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents:
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577 </conditional> |
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
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578 </conditional> |
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents:
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579 </conditional> |
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
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580 <param name="center" value="Some research center"/> |
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
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581 <assert_command> |
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents:
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changeset
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582 <has_text_matching expression="ena-upload-cli"/> |
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents:
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changeset
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583 <has_text_matching expression="--data 'paired_run_name_1.fastq.gz' 'paired_run_name_2.fastq.gz'"/> |
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents:
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changeset
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584 <has_text_matching expression="--action 'add' --center 'Some research center'"/> |
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents:
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585 <has_text_matching expression="--auto_action"/> |
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
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586 </assert_command> |
d147d6455873
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit bfc2dbccaec2ebeaf235ac833edbcead2758d792"
iuc
parents:
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587 </test> |
4
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
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diff
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|
588 <!--Test 5: build tables from user input fields NON-VIRAL samples--> |
10
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
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589 <test expect_num_outputs="5"> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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590 <conditional name="action_options"> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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591 <param name="action" value="add"/> |
1
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
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changeset
|
592 <section name="test_submit_parameters"> |
10
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
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593 <param name="submit_dev" value="False" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
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594 <param name="dry_run" value="True" /> |
1
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
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595 </section> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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596 <conditional name="input_format_conditional"> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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597 <param name="input_format" value="build_tables"/> |
10
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
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598 <param name="add_extension" value="False"/> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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|
599 <conditional name="conditional_viral_metadata"> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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|
600 <param name="viral_sample" value="False"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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changeset
|
601 <repeat name="rep_study"> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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changeset
|
602 <param name="study_title" value="Test study title"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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changeset
|
603 <param name="study_abstract" value="Test study abstract"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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changeset
|
604 <param name="study_type" value="Epigenetics"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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changeset
|
605 <param name="study_pubmed_id" value="Test study pubmedID"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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changeset
|
606 <repeat name="rep_sample"> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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changeset
|
607 <param name="sample_title" value="Test Sample title"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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changeset
|
608 <param name="sample_description" value="Test Sample description"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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changeset
|
609 <param name="scientific_name" value="Test Sample scientific name"/> |
7
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
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diff
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|
610 <param name="tax_id" value="2697049"/> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
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diff
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|
611 <param name="collection_date" value="2020"/> |
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
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|
612 <param name="geo_location_country" value="Belgium"/> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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changeset
|
613 <repeat name="rep_experiment"> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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changeset
|
614 <param name="experiment_title" value="Test experiment title"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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changeset
|
615 <param name="experiment_design" value="Test experiment design description"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
616 <param name="library_strategy" value="CTS"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
617 <param name="library_source" value="GENOMIC"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
618 <param name="library_selection" value="PCR"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
619 <param name="library_layout" value="SINGLE"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
620 <param name="insert_size" value="150"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
621 <param name="library_construction_protocol" value="Test library construction"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
622 <param name="platform" value="ILLUMINA"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
623 <param name="instrument_model" value="Illumina HiSeq 4000"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
624 <repeat name="rep_runs"> |
7
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
625 <param name="upload_files" value="1.fastqsanger.gz,sample.fq" ftype="fastqsanger.gz"/> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
626 </repeat> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
627 </repeat> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
628 </repeat> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
629 </repeat> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
630 </conditional> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
631 </conditional> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
632 </conditional> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
633 <param name="center" value="Some research center"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
634 <output name="experiments_table_out"> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
635 <assert_contents> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
636 <has_n_lines n="2"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
637 <has_n_columns n="17"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
638 </assert_contents> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
639 </output> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
640 <output name="studies_table_out"> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
641 <assert_contents> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
642 <has_n_lines n="2"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
643 <has_n_columns n="8"/> |
9
a62c4a11a67d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6770d277b4136b4068293c4260022d4ae33b2379
iuc
parents:
8
diff
changeset
|
644 <has_line_matching expression="alias\tstatus\ttitle\tstudy_type\tstudy_abstract\tpubmed_id\taccession\tsubmission_date"/> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
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|
645 </assert_contents> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
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|
646 </output> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
647 <output name="samples_table_out"> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
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|
648 <assert_contents> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
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|
649 <has_n_lines n="2"/> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
changeset
|
650 <has_n_columns n="10"/> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
651 </assert_contents> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
652 </output> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
653 <output name="runs_table_out"> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
654 <assert_contents> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
655 <has_n_lines n="3"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
656 <has_n_columns n="8"/> |
9
a62c4a11a67d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6770d277b4136b4068293c4260022d4ae33b2379
iuc
parents:
8
diff
changeset
|
657 <has_line_matching expression="alias\tstatus\texperiment_alias\tfile_name\tfile_format\taccession\tsubmission_date\tfile_checksum"/> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
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|
658 </assert_contents> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
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|
659 </output> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
660 </test> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
changeset
|
661 <!--Test 6: with submit_test to skip credentials checksRUN failing build tables from user input fields NON-VIRAL samples |
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
changeset
|
662 also tests compression of uncompressed inputs and adding the .gz suffix --> |
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
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|
663 <test expect_failure="False" expect_num_outputs="5"> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
664 <conditional name="action_options"> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
665 <param name="action" value="add"/> |
1
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
0
diff
changeset
|
666 <section name="test_submit_parameters"> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
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|
667 <param name="submit_dev" value="True" /> |
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
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|
668 <param name="dry_run" value="True" /> |
1
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
0
diff
changeset
|
669 </section> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
changeset
|
670 <param name="test_submit" value="True"/> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
671 <conditional name="input_format_conditional"> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
changeset
|
672 <param name="add_extension" value="False"/> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
673 <param name="input_format" value="build_tables"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
674 <conditional name="conditional_viral_metadata"> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
changeset
|
675 <param name="viral_sample" value="False"/> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
676 <repeat name="rep_study"> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
677 <param name="study_title" value="Test study title"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
678 <param name="study_abstract" value="Test study abstract"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
679 <param name="study_type" value="Epigenetics"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
680 <param name="study_pubmed_id" value="Test study pubmedID"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
681 <repeat name="rep_sample"> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
682 <param name="sample_title" value="Test Sample title"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
683 <param name="sample_description" value="Test Sample description"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
684 <param name="scientific_name" value="Test Sample scientific name"/> |
7
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
685 <param name="tax_id" value="2697049"/> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
changeset
|
686 <param name="collection_date" value="2020"/> |
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
changeset
|
687 <param name="geo_location_country" value="Belgium"/> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
688 <repeat name="rep_experiment"> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
689 <param name="experiment_title" value="Test experiment title"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
690 <param name="experiment_design" value="Test experiment design description"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
691 <param name="library_strategy" value="CTS"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
692 <param name="library_source" value="GENOMIC"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
693 <param name="library_selection" value="PCR"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
694 <param name="library_layout" value="SINGLE"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
695 <param name="insert_size" value="150"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
696 <param name="library_construction_protocol" value="Test library construction"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
697 <param name="platform" value="ILLUMINA"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
698 <param name="instrument_model" value="Illumina HiSeq 4000"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
699 <repeat name="rep_runs"> |
1
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
0
diff
changeset
|
700 <param name="run_base_name" value="run_from_hospital_X"/> |
7
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
701 <param name="upload_files" value="1.fastqsanger.gz,2.fastqsanger.gz" ftype="fastqsanger.gz"/> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
702 </repeat> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
703 </repeat> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
704 </repeat> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
705 </repeat> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
706 </conditional> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
707 </conditional> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
708 </conditional> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
709 <param name="center" value="Some research center"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
710 <assert_command> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
711 <has_text_matching expression="ena-upload-cli"/> |
7
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
712 <has_text_matching expression="--data '1.fastqsanger.gz' '2.fastqsanger.gz'"/> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
713 <has_text_matching expression="--action 'add' --center 'Some research center'"/> |
4
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
714 <not_has_text text="modify" /> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
715 </assert_command> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
716 </test> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
changeset
|
717 <!--Test 7: viral submission - User input metadata - Add extension = False--> |
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
changeset
|
718 <test expect_failure="False" expect_num_outputs="5"> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
719 <conditional name="action_options"> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
720 <param name="action" value="add"/> |
1
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
0
diff
changeset
|
721 <section name="test_submit_parameters"> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
changeset
|
722 <param name="submit_dev" value="False" /> |
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
changeset
|
723 <param name="dry_run" value="True" /> |
1
57251c760cab
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
0
diff
changeset
|
724 </section> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
725 <param name="test_submit" value="True"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
726 <conditional name="input_format_conditional"> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
changeset
|
727 <param name="add_extension" value="False"/> |
4
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
728 <param name="input_format" value="build_tables"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
729 <conditional name="conditional_viral_metadata"> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
changeset
|
730 <param name="viral_sample" value="True"/> |
4
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
731 <repeat name="rep_study"> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
732 <param name="study_title" value="Test study title"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
733 <param name="study_abstract" value="Test study abstract"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
734 <param name="study_type" value="Epigenetics"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
735 <param name="study_pubmed_id" value="Test study pubmedID"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
736 <repeat name="rep_sample"> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
737 <param name="sample_title" value="Test Sample title"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
738 <param name="sample_description" value="Test Sample description"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
739 <param name="scientific_name" value="Test Sample scientific name"/> |
7
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
iuc
parents:
6
diff
changeset
|
740 <param name="tax_id" value="2697049"/> |
4
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
741 <param name="collection_date" value="2020"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
742 <param name="geo_location_country" value="Belgium"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
743 <param name="host_common_name" value="Human"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
744 <param name="host_subject_id" value="Patient_001"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
745 <param name="host_health_state" value="healthy"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
746 <param name="host_sex" value="female"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
747 <param name="host_scientific_name" value="homo sapiens"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
748 <param name="collector_name" value="John The Collector"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
749 <param name="collecting_institution" value="Hospital 01"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
750 <param name="isolate" value="sample_001"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
751 <repeat name="rep_experiment"> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
752 <param name="experiment_title" value="Test experiment title"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
753 <param name="experiment_design" value="Test experiment design description"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
754 <param name="library_strategy" value="CTS"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
755 <param name="library_source" value="GENOMIC"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
756 <param name="library_selection" value="PCR"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
757 <param name="library_layout" value="SINGLE"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
758 <param name="insert_size" value="150"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
759 <param name="library_construction_protocol" value="Test library construction"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
760 <param name="platform" value="ILLUMINA"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
761 <param name="instrument_model" value="Illumina HiSeq 4000"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
762 <repeat name="rep_runs"> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
763 <param name="run_base_name" value="run_from_hospital_X"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
764 <param name="upload_files" value="1.fastqsanger.gz,2.fastqsanger.gz" ftype="fastqsanger.gz"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
765 </repeat> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
766 </repeat> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
767 </repeat> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
768 </repeat> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
769 </conditional> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
770 </conditional> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
771 </conditional> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
changeset
|
772 <param name="center" value="Some research center"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
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773 <assert_command> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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|
774 <has_text_matching expression="ena-upload-cli"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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|
775 <has_text_matching expression="--data '1.fastqsanger.gz' '2.fastqsanger.gz'"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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|
776 <has_text_matching expression="--action 'add' --center 'Some research center'"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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|
777 <has_text_matching expression="--checklist ERC000033"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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|
778 </assert_command> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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|
779 </test> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
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|
780 <!--Test 8: modify option and auto compression - viral submission - User input metadata--> |
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
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9
diff
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|
781 <test expect_failure="False" expect_num_outputs="5"> |
4
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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|
782 <conditional name="action_options"> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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783 <param name="action" value="modify"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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|
784 <section name="test_submit_parameters"> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
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785 <param name="submit_dev" value="False" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
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786 <param name="dry_run" value="True" /> |
4
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
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787 </section> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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|
788 <param name="test_submit" value="True"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
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789 <conditional name="input_format_conditional"> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
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790 <param name="add_extension" value="False"/> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
791 <param name="input_format" value="build_tables"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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|
792 <conditional name="conditional_viral_metadata"> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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|
793 <param name="viral_sample" value="True"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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|
794 <repeat name="rep_study"> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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|
795 <param name="study_title" value="Test study title"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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|
796 <param name="study_abstract" value="Test study abstract"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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|
797 <param name="study_type" value="Epigenetics"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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|
798 <param name="study_pubmed_id" value="Test study pubmedID"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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changeset
|
799 <repeat name="rep_sample"> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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changeset
|
800 <param name="sample_title" value="Test Sample title"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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|
801 <param name="sample_description" value="Test Sample description"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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|
802 <param name="scientific_name" value="Test Sample scientific name"/> |
7
6f6537780379
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
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|
803 <param name="tax_id" value="2697049"/> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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|
804 <param name="collection_date" value="2020"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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|
805 <param name="geo_location_country" value="Belgium"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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|
806 <param name="host_common_name" value="Human"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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|
807 <param name="host_subject_id" value="Patient_001"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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|
808 <param name="host_health_state" value="healthy"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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|
809 <param name="host_sex" value="female"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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|
810 <param name="host_scientific_name" value="homo sapiens"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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changeset
|
811 <param name="collector_name" value="John The Collector"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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|
812 <param name="collecting_institution" value="Hospital 01"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
813 <param name="isolate" value="sample_001"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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changeset
|
814 <repeat name="rep_experiment"> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
815 <param name="experiment_title" value="Test experiment title"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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|
816 <param name="experiment_design" value="Test experiment design description"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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|
817 <param name="library_strategy" value="CTS"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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|
818 <param name="library_source" value="GENOMIC"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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|
819 <param name="library_selection" value="PCR"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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|
820 <param name="library_layout" value="SINGLE"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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|
821 <param name="insert_size" value="150"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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|
822 <param name="library_construction_protocol" value="Test library construction"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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|
823 <param name="platform" value="ILLUMINA"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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|
824 <param name="instrument_model" value="Illumina HiSeq 4000"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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|
825 <repeat name="rep_runs"> |
1
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ffea061c1ad6e7291abfe220230dbdbe8d19a2bd"
iuc
parents:
0
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|
826 <param name="run_base_name" value="run_from_hospital_X"/> |
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|
827 <param name="upload_files" value="1.fastqsanger.gz,2.fastqsanger.gz" ftype="fastqsanger.gz"/> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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changeset
|
828 </repeat> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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changeset
|
829 </repeat> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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|
830 </repeat> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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|
831 </repeat> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
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|
832 </conditional> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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|
833 </conditional> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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|
834 </conditional> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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changeset
|
835 <param name="center" value="Some research center"/> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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|
836 <assert_command> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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|
837 <has_text_matching expression="ena-upload-cli"/> |
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480d9e9d156b
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9
diff
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|
838 <has_text_matching expression="--data '1.fastqsanger.gz' '2.fastqsanger.gz'"/> |
4
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
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|
839 <has_text_matching expression="--action 'modify' --center 'Some research center'"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
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|
840 <has_text_matching expression="--checklist ERC000033"/> |
26ccb678abc8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit ba358013c83e7dfffec895946d36585f237e54c5"
iuc
parents:
3
diff
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|
841 <not_has_text text="add" /> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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|
842 </assert_command> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
843 </test> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
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|
844 </tests> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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|
845 <help><![CDATA[ |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
846 This is a wrapper for the ENA upload tool in https://github.com/usegalaxy-eu/ena-upload-cli |
10
480d9e9d156b
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iuc
parents:
9
diff
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|
847 The input metadata can be submitted following the tabular format of the templates or their excel spreadsheet equivalent in https://github.com/ELIXIR-Belgium/ENA-metadata-templates. This template repo provides ready to use sheets for every ENA sample checklist and is automatically updated. |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
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|
848 ]]></help> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
849 <citations> |
10
480d9e9d156b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
iuc
parents:
9
diff
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|
850 <citation type="doi">doi:10.1093/bioinformatics/btab421</citation> |
0
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
851 </citations> |
382518f24d6d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 57b434bcf493554d060a99b65e66f274d5c00e0a"
iuc
parents:
diff
changeset
|
852 </tool> |