Mercurial > repos > devteam > data_manager_fetch_genome_dbkeys_all_fasta
annotate data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml @ 3:86fa71e9b427 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
author | devteam |
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date | Fri, 26 Aug 2016 12:46:47 -0400 |
parents | 776bb1b478a0 |
children | 60994ca04177 |
rev | line source |
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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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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-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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3 <command><![CDATA[ |
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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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4 python "$__tool_directory__"/data_manager_fetch_genome_all_fasta_dbkeys.py "${out_file}" |
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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5 #if str( $dbkey_source.dbkey_source_selector ) == '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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6 --dbkey_description ${ dbkey_source.dbkey.get_display_text() } |
86fa71e9b427
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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7 #else |
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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit 9df6291d7d65c5274c4fd35775108eae58ea6c23
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8 --dbkey_description "${ dbkey_source.dbkey_name or $dbkey_source.dbkey }" |
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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9 #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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10 ]]></command> |
0 | 11 <inputs> |
12 <conditional name="dbkey_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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13 <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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14 <option value="existing" selected="True">Existing</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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15 <option value="new">New</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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16 </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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17 <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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18 <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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19 </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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20 <when value="new"> |
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 <param type="text" name="dbkey" value="" label="dbkey" optional="False" /> |
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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22 <param type="text" name="dbkey_name" value="" label="Display name for dbkey" /> |
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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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23 </when> |
0 | 24 </conditional> |
25 <param type="text" name="sequence_name" value="" label="Name of sequence" /> | |
26 <param type="text" name="sequence_id" value="" label="ID for sequence" /> | |
27 <conditional name="reference_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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28 <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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29 <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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30 <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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31 <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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32 <option value="history">History</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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33 <option value="directory">Directory on Server</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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34 </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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35 <when value="ucsc"> |
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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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36 <param type="text" name="requested_dbkey" value="" label="UCSC's DBKEY for source FASTA" optional="False" /> |
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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37 </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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38 <when value="ncbi"> |
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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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39 <param type="text" name="requested_identifier" value="" label="NCBI identifier/accession" help="Identifiers (e.g 667699573) or accessions (e.g AC020606.7) may be used" optional="False" /> |
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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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40 </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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41 <when value="url"> |
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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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42 <param type="text" area="True" name="user_url" value="http://" label="URLs" optional="False" /> |
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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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43 </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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44 <when value="history"> |
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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 <param name="input_fasta" type="data" format="fasta" label="FASTA File" multiple="False" optional="False" /> |
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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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46 </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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47 <when value="directory"> |
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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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48 <param type="text" name="fasta_filename" value="" label="Full path to FASTA File on disk" optional="False" /> |
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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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49 <param type="boolean" name="create_symlink" truevalue="create_symlink" falsevalue="copy_file" label="Create symlink to original data instead of copying" checked="False" /> |
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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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50 </when> |
0 | 51 </conditional> |
52 <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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53 <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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54 <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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55 <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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56 <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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57 <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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58 </param> |
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59 <when value="as_is"> |
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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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60 </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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61 <when value="lexicographical"> |
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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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62 </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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63 <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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64 </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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65 <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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66 <repeat name="sequence_identifiers" title="Sequence Identifiers" min="1" default="1"> |
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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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67 <param type="text" name="identifier" value="" label="Sequence Identifier" optional="False" /> |
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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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68 </repeat> |
0 | 69 <param name="handle_not_listed_selector" type="select" label="How to handle non-specified Identifiers"> |
70 <option value="discard" selected="True">Discard</option> | |
71 <option value="keep_append">Keep and Append</option> | |
72 <option value="keep_prepend">Keep and Prepend</option> | |
73 </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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74 </when> |
0 | 75 </conditional> |
76 </inputs> | |
77 <outputs> | |
78 <data name="out_file" format="data_manager_json"/> | |
79 </outputs> | |
80 <tests> | |
81 <!-- TODO: need some way to test that new entry was added to data table --> | |
82 <test> | |
83 <param name="dbkey" value="anoGam1"/> | |
84 <param name="sequence_name" value=""/> | |
85 <param name="sequence_desc" value=""/> | |
86 <param name="sequence_id" value=""/> | |
87 <param name="reference_source_selector" value="history"/> | |
88 <param name="input_fasta" value="phiX174.fasta"/> | |
89 <param name="sort_selector" value="as_is"/> | |
90 <output name="out_file" file="phiX174.data_manager_json"/> | |
91 </test> | |
92 </tests> | |
93 <help> | |
94 **What it does** | |
95 | |
96 Fetches a reference genome from various sources (UCSC, NCBI, URL, Galaxy History, or a server directory) and populates the "all_fasta" data table. | |
97 | |
98 ------ | |
99 | |
100 | |
101 | |
102 .. class:: infomark | |
103 | |
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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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104 **Notice:** If you leave name, description, or id blank, it will be generated automatically. |
0 | 105 |
106 </help> | |
107 </tool> |