Mercurial > repos > cpt > cpt_type_filter
diff cpt_type_filter/filter_type.xml @ 0:e912e40d2f86 draft
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author | cpt |
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date | Fri, 13 May 2022 18:05:32 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_type_filter/filter_type.xml Fri May 13 18:05:32 2022 +0000 @@ -0,0 +1,56 @@ +<?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>