Mercurial > repos > jjohnson > gffutils
diff create_gffdb.xml @ 1:8880c2e4b2ee draft
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit eeb6499c828d0a99b6a891ed88de690cc1b8aeed-dirty
| author | jjohnson |
|---|---|
| date | Mon, 16 Apr 2018 18:14:30 -0400 |
| parents | 8ba71aead5bc |
| children | b956465b8893 |
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--- a/create_gffdb.xml Sun Apr 08 13:26:47 2018 -0400 +++ b/create_gffdb.xml Mon Apr 16 18:14:30 2018 -0400 @@ -1,13 +1,21 @@ -<tool id="create_gffdb" name="Create GFF DB for GTF or GFF3" version="0.1.0"> - <description>gffutils sqlite db</description> +<tool id="create_gffdb" name="Create gffutils SQLite DB" version="0.1.0"> + <description>for GTF or GFF3</description> <requirements> <requirement type="package">gffutils</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - python '$__tool_directory__/create_gffdb.py' '$input' '$output' + python '$__tool_directory__/create_gffdb.py' $create_introns '$input' '$output' ]]></command> <inputs> <param name="input" type="data" format="gtf,gff3" label="GTF or GFF3 Annotation"/> + <param name="create_introns" type="boolean" truevalue="--create_introns" falsevalue="" checked="false" + label="create intron features"/> + <param name="disable_infer_transcripts" type="boolean" truevalue="--disable_infer_transcripts" falsevalue="" checked="true" + label="disable_infer_transcripts (True for Ensmbl GTF)" + help="Can be more than 100 times slower if this is false"/> + <param name="disable_infer_genes" type="boolean" truevalue="--disable_infer_genes" falsevalue="" checked="true" + label="disable_infer_transcripts (True for Ensmbl GTF)" + help="Can be more than 100 times slower if this is false"/> </inputs> <outputs> <data name="output" format="sqlite" label="${tool.name} ${input.name}.sqlite" /> @@ -23,5 +31,7 @@ </test> </tests> <help><![CDATA[ +Creates a SQLite database for a GTF or GFF3 feature file. +http://daler.github.io/gffutils/index.html ]]></help> </tool>