Mercurial > repos > bebatut > data_manager_humann2_database_downloader
changeset 9:cb9dac6233f2 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_humann2_database_downloader commit 76f55682bf146c34d786bda2a6d3b7f0aed0faa9-dirty
| author | bebatut |
|---|---|
| date | Tue, 13 Jun 2017 02:47:14 -0400 |
| parents | a0eed08a6b61 |
| children | 023350005f5e |
| files | data_manager/data_manager_humann2_download.py data_manager/data_manager_humann2_download.xml data_manager/macros.xml |
| diffstat | 3 files changed, 16 insertions(+), 12 deletions(-) [+] |
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--- a/data_manager/data_manager_humann2_download.py Thu Mar 02 09:19:25 2017 -0500 +++ b/data_manager/data_manager_humann2_download.py Tue Jun 13 02:47:14 2017 -0400 @@ -15,7 +15,7 @@ "uniref50_diamond": "Full UniRef50", "uniref50_ec_filtered_diamond": "EC-filtered UniRef50", "uniref50_GO_filtered_rapsearch2": "GO filtered UniRef50 for rapsearch2", - "uniref90_diamond": "Full UniRef50", + "uniref90_diamond": "Full UniRef90", "uniref90_ec_filtered_diamond": "EC-filtered UniRef90", "DEMO_diamond": "Demo" }
--- a/data_manager/data_manager_humann2_download.xml Thu Mar 02 09:19:25 2017 -0500 +++ b/data_manager/data_manager_humann2_download.xml Tue Jun 13 02:47:14 2017 -0400 @@ -1,17 +1,20 @@ -<tool id="data_manager_humann2_download" name="HUMAnN2 download" version="0.9.9" tool_type="manage_data"> +<tool id="data_manager_humann2_download" name="HUMAnN2 download" version="@VERSION@.0" tool_type="manage_data"> <description>Download HUMAnN2 database</description> + <macros> + <token name="@VERSION@">0.9.9</token> + </macros> <requirements> - <requirement type="package" version="0.9.9">humann2</requirement> + <requirement type="package" version="@VERSION@">humann2</requirement> </requirements> <stdio> <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> <exit_code range="1:" level="fatal" description="Error" /> </stdio> - <command interpreter="python"> - data_manager_humann2_download.py + <command> + python '$__tool_directory__/data_manager_humann2_download.py' --database '$db.database' - --build '$db.build' - "${out_file}" + --build $db.build + '${out_file}' </command> <inputs> <conditional name="db"> @@ -38,19 +41,16 @@ </conditional> </inputs> <outputs> - <data name="out_file" format="data_manager_json" label="${tool.name}"/> + <data name="out_file" format="data_manager_json" label="${tool.name}" /> </outputs> <tests> </tests> <help> - This tool downloads the HUMAnN2 databases. -For details about this tool, please go to http://gemini.readthedocs.org - +Read more about the tool at http://huttenhower.sph.harvard.edu/humann2/manual . </help> <citations> <citation type="doi">10.1371/journal.pcbi.1003153</citation> - <yield /> </citations> </tool>