Mercurial > repos > petr-novak > repeat_annotation_pipeline3

comparison compare_gff.xml @ 6:b53f5a456d01 draft

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"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
author petr-novak
date Thu, 19 May 2022 08:23:55 +0000
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children 5366d5ea04bc
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5:eca9213923b1 6:b53f5a456d01
1 <tool id="compare_gff" name="Compare overlap of two GFF3" version="0.1.0" python_template_version="3.5">
2 <requirements>
3 <requirement type="package">bioconductor-rtracklayer</requirement>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6 $__tool_directory__/compare_gff.R '$input1_gff' '$input2_gff' '$attribute_name'
7 &&
8 cp annotation_overlap_long.csv '$out_long'
9 &&
10 cp annotation_overlap.csv '$out_wide'
11
12 ]]></command>
13 <inputs>
14 <param type="data" name="input1_gff" format="gff" label="First GFF">
15 <sanitizer invalid_char="">
16 <valid initial="string.ascii_letters,string.digits">
17 <add value="_" />
18 </valid>
19 </sanitizer>
20 </param>
21 <param type="data" name="input2_gff" format="gff" label="Second GFF">
22 <sanitizer invalid_char="">
23 <valid initial="string.ascii_letters,string.digits">
24 <add value="_" />
25 </valid>
26 </sanitizer>
27 </param>
28 <param type="text" name="attribute_name" label="Name of attribute to summarize"/>
29 </inputs>
30 <outputs>
31 <data name="out_long" format="tabular" label="Overlap of annotations
32 ${input1_gff.hid} and ${input1_gff.hid} (as matrix)" />
33 <data name="out_wide" format="tabular" label="Overlap of annotations
34 ${input1_gff.hid} and ${input1_gff.hid} (as table)"/>
35 </outputs>
36 <help><![CDATA[
37 Compare overlaps in two GFF3 by selected attribute. Overlap is reported a number of bases. It expects not overlap within individuals GFF3.
38 ]]></help>
39 </tool>