|
0
|
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>
|
