Mercurial > repos > guerler > dbkit
comparison dbkit_create.xml @ 0:1914107cc967 draft
"planemo upload commit 3632646bec5edbe47e06c894e32bfd215b895555-dirty"
| author | guerler |
|---|---|
| date | Wed, 25 Nov 2020 17:22:48 +0000 |
| parents | |
| children | 987e55ea29b8 |
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| -1:000000000000 | 0:1914107cc967 |
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| 1 <tool id="dbkit_create" name="DBKit Create" version="0.1.1" python_template_version="3.5" license="MIT"> | |
| 2 <description>database generator</description> | |
| 3 <command detect_errors="exit_code"><![CDATA[ | |
| 4 mkdir temp && | |
| 5 python3 '$__tool_directory__/dbkit_create.py' -l '$input' -u '$url' -t 'temp' -o '$index' -d '$database' -g '$log' -il '$advanced.idlength' -ic '$advanced.idcase' -ie '$advanced.idextension' | |
| 6 ]]></command> | |
| 7 <inputs> | |
| 8 <param format="tabular" name="input" type="data" label="List of Identifiers" help="Specify a list containing all entry identifiers to be downloaded."/> | |
| 9 <param name="url" type="text" label="URL to External Source" help="Specify the URL to the external database source."> | |
| 10 <option value="https://files.rcsb.org/download/">https://files.rcsb.org/download/</option> | |
| 11 </param> | |
| 12 <conditional name="advanced"> | |
| 13 <param name="type" type="boolean" label="Identifier Formatting Options" /> | |
| 14 <when value="true"> | |
| 15 <param name="idextension" type="text" label="Identifier Extensions" help="Specify the extension of the identifier (optional)."/> | |
| 16 <param name="idlength" type="integer" label="Identifier Length" value="0" min="0" max="20" help="Specify the length of the identifier (disable=0)."/> | |
| 17 <param name="idcase" type="select" label="Identifier Case" display="radio" help="Choose to format the identifier by changing its case (optional)."> | |
| 18 <option value="">Unformatted</option> | |
| 19 <option value="lower">Lower</option> | |
| 20 <option value="upper">Upper</option> | |
| 21 </param> | |
| 22 </when> | |
| 23 <when value="false"> | |
| 24 <param name="idextension" type="hidden" value="" /> | |
| 25 <param name="idlength" type="hidden" value="0" /> | |
| 26 <param name="idcase" type="hidden" value="" /> | |
| 27 </when> | |
| 28 </conditional> | |
| 29 </inputs> | |
| 30 <outputs> | |
| 31 <data format="ffindex" name="index" label="DBKit Index"/> | |
| 32 <data format="ffdata" name="database" label="DBKit Database" /> | |
| 33 <data format="txt" name="log" label="DBKit Log" /> | |
| 34 </outputs> | |
| 35 <tests> | |
| 36 <test> | |
| 37 <param name="input" value="create/chains.tabular" /> | |
| 38 <param name="url" value="https://files.rcsb.org/download/" /> | |
| 39 <conditional name="advanced"> | |
| 40 <param name="type" value="true" /> | |
| 41 <param name="idextension" value="pdb" /> | |
| 42 <param name="idlength" value="4" /> | |
| 43 <param name="idcase" value="lower" /> | |
| 44 </conditional> | |
| 45 <param format="tabular" name="database" value="roc/biogrid_fret.txt" /> | |
| 46 <output name="index" file="create/index.ffindex" /> | |
| 47 <output name="database" file="create/data.ffdata" /> | |
| 48 </test> | |
| 49 </tests> | |
| 50 <help><![CDATA[ | |
| 51 This database creation tool downloads entries from an external resource and creates a datasets with all its contents. Additionally an index file is | |
| 52 generated indicating the start and end of every entry within the database file. | |
| 53 ]]></help> | |
| 54 </tool> |