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comparison filter_type.xml @ 3:3df8d991938a draft

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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:53:47 +0000
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2:4f44b49e3f5e 3:3df8d991938a
1 <tool id="edu.tamu.cpt.gff3.filter_type" name="GFF3 Feature Type Filter" version="19.1.0.0">
2 <description>selects features from a gff3 file based on feature type</description>
3 <macros>
4 <import>macros.xml</import>
5 <import>cpt-macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command detect_errors="aggressive"><![CDATA[
9 #set repeat_data = '" "'.join([ str($var.type) for $var in $repeat_0 ])
10
11 'python $__tool_directory__/filter_type.py'
12 @INPUT_GFF@
13 "$repeat_data"
14 '$invert'
15 > '$output']]></command>
16 <inputs>
17 <expand macro="gff3_input"/>
18 <repeat name="repeat_0" title="Feature Types">
19 <param label="Feature type" name="type" type="text"/>
20 </repeat>
21 <param checked="true" label="Invert the filter" name="invert" type="boolean" truevalue="--invert" falsevalue=""/>
22 </inputs>
23 <outputs>
24 <data format="gff3" name="output"/>
25 </outputs>
26 <tests>
27 <test>
28 <param name="gff3_data" value="Miro_FilterIn.gff3"/>
29 <param name="repeat_0_0|type" value="CDS"/>
30 <param name="invert" value="False"/>
31 <output name="output" file="Miro_FilterOut1.gff3"/>
32 </test>
33 <test>
34 <param name="gff3_data" value="Miro_FilterIn.gff3"/>
35 <param name="repeat_0_0|type" value="CDS"/>
36 <param name="invert" value="--invert"/>
37 <output name="output" file="Miro_FilterOut2.gff3"/>
38 </test>
39 </tests>
40 <help><![CDATA[
41 **What it does**
42
43 The tool finds the specified feature type(s) in an input GFF3 and will output
44 **only** the specified feature type. By selecting the inversion, **everything except**
45 the specified feature type(s) will be included in the output GFF3.
46
47 For example, user may output **only** ``Shine_Dalgarno_sequence`` type features, or,
48 inverting that, output everything but ``Shine_Dalgarno_sequence`` type features. Any
49 feature type used in the input GFF3 can be filtered; typical options would include gene,
50 mRNA, CDS, tRNA, and terminator. The input name format must follow sequence ontology
51 convention (http://www.sequenceontology.org/).
52
53 ]]></help>
54 <expand macro="citations"/>
55 </tool>