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comparison cpt_type_filter/filter_type.xml @ 0:e912e40d2f86 draft

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author cpt
date Fri, 13 May 2022 18:05:32 +0000
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1 <?xml version="1.0"?>
2 <tool id="edu.tamu.cpt.gff3.filter_type" name="GFF3 Feature Type Filter" version="19.1.0.0">
3 <description>selects features from a gff3 file based on feature type</description>
4 <macros>
5 <import>macros.xml</import>
6 <import>cpt-macros.xml</import>
7 </macros>
8 <expand macro="requirements"/>
9 <command detect_errors="aggressive"><![CDATA[
10 #set repeat_data = '" "'.join([ str($var.type) for $var in $repeat_0 ])
11
12 python $__tool_directory__/filter_type.py
13 @INPUT_GFF@
14 "$repeat_data"
15 $invert
16 > $output]]></command>
17 <inputs>
18 <expand macro="gff3_input" />
19 <repeat name="repeat_0" title="Feature Types">
20 <param label="Feature type" name="type" type="text"/>
21 </repeat>
22 <param checked="true" label="Invert the filter" name="invert" type="boolean" truevalue="--invert" falsevalue="" />
23 </inputs>
24 <outputs>
25 <data format="gff3" name="output"/>
26 </outputs>
27 <tests>
28 <test>
29 <param name="gff3_data" value="Miro_FilterIn.gff3" />
30 <param name="repeat_0_0|type" value="CDS" />
31 <param name="invert" value="False" />
32 <output name="output" file="Miro_FilterOut1.gff3" />
33 </test>
34 <test>
35 <param name="gff3_data" value="Miro_FilterIn.gff3" />
36 <param name="repeat_0_0|type" value="CDS" />
37 <param name="invert" value="--invert" />
38 <output name="output" file="Miro_FilterOut2.gff3" />
39 </test>
40 </tests>
41 <help><![CDATA[
42 **What it does**
43
44 The tool finds the specified feature type(s) in an input GFF3 and will output
45 **only** the specified feature type. By selecting the inversion, **everything except**
46 the specified feature type(s) will be included in the output GFF3.
47
48 For example, user may output **only** ``Shine_Dalgarno_sequence`` type features, or,
49 inverting that, output everything but ``Shine_Dalgarno_sequence`` type features. Any
50 feature type used in the input GFF3 can be filtered; typical options would include gene,
51 mRNA, CDS, tRNA, and terminator. The input name format must follow sequence ontology
52 convention (http://www.sequenceontology.org/).
53
54 ]]></help>
55 <expand macro="citations" />
56 </tool>