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author | cpt |
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date | Fri, 13 May 2022 18:05:32 +0000 |
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<?xml version="1.0"?> <tool id="edu.tamu.cpt.gff3.filter_type" name="GFF3 Feature Type Filter" version="19.1.0.0"> <description>selects features from a gff3 file based on feature type</description> <macros> <import>macros.xml</import> <import>cpt-macros.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="aggressive"><![CDATA[ #set repeat_data = '" "'.join([ str($var.type) for $var in $repeat_0 ]) python $__tool_directory__/filter_type.py @INPUT_GFF@ "$repeat_data" $invert > $output]]></command> <inputs> <expand macro="gff3_input" /> <repeat name="repeat_0" title="Feature Types"> <param label="Feature type" name="type" type="text"/> </repeat> <param checked="true" label="Invert the filter" name="invert" type="boolean" truevalue="--invert" falsevalue="" /> </inputs> <outputs> <data format="gff3" name="output"/> </outputs> <tests> <test> <param name="gff3_data" value="Miro_FilterIn.gff3" /> <param name="repeat_0_0|type" value="CDS" /> <param name="invert" value="False" /> <output name="output" file="Miro_FilterOut1.gff3" /> </test> <test> <param name="gff3_data" value="Miro_FilterIn.gff3" /> <param name="repeat_0_0|type" value="CDS" /> <param name="invert" value="--invert" /> <output name="output" file="Miro_FilterOut2.gff3" /> </test> </tests> <help><![CDATA[ **What it does** The tool finds the specified feature type(s) in an input GFF3 and will output **only** the specified feature type. By selecting the inversion, **everything except** the specified feature type(s) will be included in the output GFF3. For example, user may output **only** ``Shine_Dalgarno_sequence`` type features, or, inverting that, output everything but ``Shine_Dalgarno_sequence`` type features. Any feature type used in the input GFF3 can be filtered; typical options would include gene, mRNA, CDS, tRNA, and terminator. The input name format must follow sequence ontology convention (http://www.sequenceontology.org/). ]]></help> <expand macro="citations" /> </tool>