Mercurial > repos > iuc > data_manager_humann2_database_downloader
annotate data_manager/data_manager_humann2_download.xml @ 0:048593e41359 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
author | iuc |
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date | Sun, 12 Mar 2017 14:33:34 -0400 |
parents | |
children | 1316375a8cbb |
rev | line source |
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0
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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changeset
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1 <tool id="data_manager_humann2_download" name="HUMAnN2 download" version="0.9.9" tool_type="manage_data"> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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2 <description>Download HUMAnN2 database</description> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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3 <requirements> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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4 <requirement type="package" version="0.9.9">humann2</requirement> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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5 </requirements> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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6 <stdio> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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7 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
diff
changeset
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8 <exit_code range="1:" level="fatal" description="Error" /> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
diff
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9 </stdio> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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10 <command interpreter="python"> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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11 data_manager_humann2_download.py |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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12 --database '$db.database' |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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13 --build '$db.build' |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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14 '${out_file}' |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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15 </command> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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16 <inputs> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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17 <conditional name="db"> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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18 <param name="database" type="select" label="Type of database to download"> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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19 <option value="chocophlan" selected="true">Nucleotide database</option> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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20 <option value="uniref">Protein database</option> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
diff
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21 </param> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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22 <when value="chocophlan"> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
diff
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23 <param name="build" type="select" label="Build for nucleotide database"> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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24 <option value="full" selected="true">Full</option> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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changeset
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25 <option value="DEMO">Demo</option> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
diff
changeset
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26 </param> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
diff
changeset
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27 </when> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
diff
changeset
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28 <when value="uniref"> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
diff
changeset
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29 <param name="build" type="select" label="Build for protein database"> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
diff
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30 <option value="uniref50_diamond">Full UniRef50</option> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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31 <option value="uniref50_ec_filtered_diamond">EC-filtered UniRef50</option> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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32 <option value="uniref50_GO_filtered_rapsearch2">GO filtered UniRef50 for rapsearch2</option> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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33 <option value="uniref90_diamond" selected="true">Full UniRef50</option> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
diff
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34 <option value="uniref90_ec_filtered_diamond">EC-filtered UniRef90</option> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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35 <option value="DEMO_diamond">Demo</option> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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36 </param> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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37 </when> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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38 </conditional> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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39 </inputs> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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40 <outputs> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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41 <data name="out_file" format="data_manager_json" label="${tool.name}"/> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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42 </outputs> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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43 <tests> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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44 </tests> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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45 <help> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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46 |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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47 This tool downloads the HUMAnN2 databases. |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
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48 |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
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49 `Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_. |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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50 |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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51 </help> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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52 <citations> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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53 <citation type="doi">10.1371/journal.pcbi.1003153</citation> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
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54 <yield /> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
parents:
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55 </citations> |
048593e41359
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 3e179ac4ab2051414320b3811540dfc9b0966061
iuc
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56 </tool> |