Mercurial > repos > guerler > ffindex_dbkit_create
comparison dbkit_create.xml @ 0:8b48a608f1df draft
"planemo upload commit b68cb41b1884703c4f1574b65a6408d7d0cca321"
| author | guerler |
|---|---|
| date | Tue, 23 Mar 2021 23:06:15 +0000 |
| parents | |
| children | c1dff5c2a7b3 |
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| -1:000000000000 | 0:8b48a608f1df |
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| 1 <tool id="ffindex_dbkit_create" name="DBKit Create" version="0.1.1" license="MIT" profile="20.01"> | |
| 2 <description>database</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 8 mkdir -p inputs && | |
| 9 #for item in $inputs | |
| 10 ln -s '${item}' 'inputs/${item.element_identifier}' && | |
| 11 #end for | |
| 12 dbkit_create.py | |
| 13 -l '$input' | |
| 14 -p 'inputs' | |
| 15 -o '$index' | |
| 16 -d '$database' | |
| 17 -g '$log' | |
| 18 -il '$advanced.idlength' | |
| 19 -ic '$advanced.idcase' | |
| 20 -ie '$advanced.idextension' | |
| 21 ]]> </command> | |
| 22 <inputs> | |
| 23 <param name="input" type="data" format="tabular" label="List of Identifiers" help="Specify a list containing all entry identifiers to be downloaded." /> | |
| 24 <param name="inputs" type="data" format="txt" multiple="true" label="Specify your datasets" help="The datasets that you want to convert into an ffindex." /> | |
| 25 <conditional name="advanced"> | |
| 26 <param name="type" type="select" label="Identifier Formatting Options" help=""> | |
| 27 <option value="true">Yes, I want to format my identifiers</option> | |
| 28 <option value="false">No formatting</option> | |
| 29 </param> | |
| 30 <when value="true"> | |
| 31 <param name="idextension" type="text" optional="true" label="Identifier Extensions" help="Specify the extension of the identifier" /> | |
| 32 <param name="idlength" type="integer" label="Identifier Length" value="0" min="0" max="20" help="Specify the length of the identifier (disable=0)." /> | |
| 33 <param name="idcase" type="select" label="Identifier Case" display="radio" help="Choose to format the identifier by changing its case (optional)."> | |
| 34 <option value="">Unformatted</option> | |
| 35 <option value="lower">Lower</option> | |
| 36 <option value="upper">Upper</option> | |
| 37 </param> | |
| 38 </when> | |
| 39 <when value="false"> | |
| 40 <param name="idextension" type="hidden" value="" /> | |
| 41 <param name="idlength" type="hidden" value="0" /> | |
| 42 <param name="idcase" type="hidden" value="" /> | |
| 43 </when> | |
| 44 </conditional> | |
| 45 <expand macro="logfile" /> | |
| 46 </inputs> | |
| 47 <outputs> | |
| 48 <data name="index" format="ffindex" label="DBKit Index" /> | |
| 49 <data name="database" format="ffdata" label="DBKit Database" /> | |
| 50 <data format="txt" name="log" label="DBKit Log"> | |
| 51 <filter>logfile</filter> | |
| 52 </data> | |
| 53 </outputs> | |
| 54 <tests> | |
| 55 <test> | |
| 56 <param name="input" value="create/sequences.tabular" ftype="tabular" /> | |
| 57 <param name="inputs" value="create/NP_000282.1.hhr,create/NP_000290.2.hhr,create/NP_000548.2.hhr,create/NP_000836.2.hhr" /> | |
| 58 <conditional name="advanced"> | |
| 59 <param name="type" value="false" /> | |
| 60 </conditional> | |
| 61 <output name="index" file="create/sequences.ffindex" ftype="ffindex" /> | |
| 62 <output name="database" file="create/sequences.ffdata" ftype="ffdata" /> | |
| 63 </test> | |
| 64 </tests> | |
| 65 <help><![CDATA[ | |
| 66 | |
| 67 **What it does** | |
| 68 | |
| 69 This database creation tool downloads entries from an external resource and creates a datasets with all its contents. Additionally an index file is | |
| 70 generated indicating the start and size of every entry within the database file. The tool can also operate on collections. | |
| 71 ]]> </help> | |
| 72 <expand macro="citations" /> | |
| 73 </tool> |