Mercurial > repos > devteam > data_manager_fetch_genome_dbkeys_all_fasta
annotate data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml @ 5:a246b4f11133 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f-dirty
author | iuc |
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date | Wed, 05 Apr 2017 08:33:57 -0400 |
parents | 60994ca04177 |
children | 16ab4dd6a0e5 |
rev | line source |
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86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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1 <tool id="data_manager_fetch_genome_all_fasta_dbkey" name="Create DBKey and Reference Genome" version="0.0.2" tool_type="manage_data"> |
0 | 2 <description>fetching</description> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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3 <command detect_errors="exit_code"><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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4 python '$__tool_directory__/data_manager_fetch_genome_all_fasta_dbkeys.py' |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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5 '${out_file}' |
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86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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6 #if str( $dbkey_source.dbkey_source_selector ) == 'existing': |
5
a246b4f11133
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f-dirty
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7 --dbkey_description ${ dbkey_source.dbkey.get_display_text() } |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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8 #else |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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9 --dbkey_description '${ dbkey_source.dbkey_name or $dbkey_source.dbkey }' |
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86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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10 #end if |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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11 ]]></command> |
0 | 12 <inputs> |
13 <conditional name="dbkey_source"> | |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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14 <param name="dbkey_source_selector" type="select" label="Use existing dbkey or create a new one."> |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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15 <option value="existing" selected="True">Existing</option> |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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16 <option value="new">New</option> |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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17 </param> |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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18 <when value="existing"> |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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19 <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" /> |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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20 </when> |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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21 <when value="new"> |
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60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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22 <param name="dbkey" type="text" value="" optional="false" label="dbkey" /> |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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23 <param name="dbkey_name" type="text" value="" label="Display name for dbkey" /> |
3
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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24 </when> |
0 | 25 </conditional> |
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60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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26 <param name="sequence_name" type="text" value="" label="Name of sequence" /> |
60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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27 <param name="sequence_id" type="text" value="" label="ID for sequence" /> |
0 | 28 <conditional name="reference_source"> |
3
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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29 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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30 <option value="ucsc" selected="True">UCSC</option> |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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31 <option value="ncbi">NCBI</option> |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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32 <option value="url">URL</option> |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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33 <option value="history">History</option> |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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34 <option value="directory">Directory on Server</option> |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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35 </param> |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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36 <when value="ucsc"> |
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60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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37 <param name="requested_dbkey" type="text" value="" optional="false" label="UCSC's DBKEY for source FASTA" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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38 </when> |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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39 <when value="ncbi"> |
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60994ca04177
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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40 <param name="requested_identifier" type="text" value="" optional="false" label="NCBI identifier/accession" help="Identifiers (e.g 667699573) or accessions (e.g AC020606.7) may be used" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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41 </when> |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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42 <when value="url"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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43 <param name="user_url" type="text" area="True" value="http://" optional="false" label="URLs" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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44 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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45 <when value="history"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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46 <param name="input_fasta" type="data" format="fasta" label="FASTA file" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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47 </when> |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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48 <when value="directory"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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49 <param name="fasta_filename" type="text" value="" optional="false" label="Full path to FASTA file on disk" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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50 <param name="create_symlink" type="boolean" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to original data instead of copying" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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51 </when> |
0 | 52 </conditional> |
53 <conditional name="sorting"> | |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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54 <param name="sort_selector" type="select" label="Sort by chromosome name"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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55 <option value="as_is" selected="True">As is</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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56 <option value="lexicographical">Lexicographical</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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57 <option value="gatk">GATK</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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58 <option value="custom">Custom</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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59 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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60 <when value="as_is" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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61 <when value="lexicographical" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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62 <when value="gatk" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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63 <when value="custom"> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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64 <repeat name="sequence_identifiers" title="Sequence Identifiers" min="1" default="1"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 8652f36a3a3838dca989426961561e81432acf4f
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65 <param name="identifier" type="text" value="" optional="false" label="Sequence Identifier" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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66 </repeat> |
0 | 67 <param name="handle_not_listed_selector" type="select" label="How to handle non-specified Identifiers"> |
68 <option value="discard" selected="True">Discard</option> | |
69 <option value="keep_append">Keep and Append</option> | |
70 <option value="keep_prepend">Keep and Prepend</option> | |
71 </param> | |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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72 </when> |
0 | 73 </conditional> |
74 </inputs> | |
75 <outputs> | |
76 <data name="out_file" format="data_manager_json"/> | |
77 </outputs> | |
78 <tests> | |
79 <!-- TODO: need some way to test that new entry was added to data table --> | |
80 <test> | |
81 <param name="dbkey" value="anoGam1"/> | |
82 <param name="sequence_name" value=""/> | |
83 <param name="sequence_id" value=""/> | |
84 <param name="reference_source_selector" value="history"/> | |
85 <param name="input_fasta" value="phiX174.fasta"/> | |
86 <param name="sort_selector" value="as_is"/> | |
87 <output name="out_file" file="phiX174.data_manager_json"/> | |
88 </test> | |
89 </tests> | |
90 <help> | |
91 **What it does** | |
92 | |
93 Fetches a reference genome from various sources (UCSC, NCBI, URL, Galaxy History, or a server directory) and populates the "all_fasta" data table. | |
94 | |
95 ------ | |
96 | |
97 .. class:: infomark | |
98 | |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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99 **Notice:** If you leave name, description, or id blank, it will be generated automatically. |
0 | 100 </help> |
101 </tool> |