Mercurial > repos > petr-novak > repeat_annotation_pipeline3
annotate compare_gff.xml @ 10:276efc4cb17f draft
Uploaded
author | petr-novak |
---|---|
date | Thu, 04 May 2023 09:27:43 +0000 |
parents | b53f5a456d01 |
children | 5366d5ea04bc |
rev | line source |
---|---|
6
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
1 <tool id="compare_gff" name="Compare overlap of two GFF3" version="0.1.0" python_template_version="3.5"> |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
2 <requirements> |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
3 <requirement type="package">bioconductor-rtracklayer</requirement> |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
4 </requirements> |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
5 <command detect_errors="exit_code"><![CDATA[ |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
6 $__tool_directory__/compare_gff.R '$input1_gff' '$input2_gff' '$attribute_name' |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
7 && |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
8 cp annotation_overlap_long.csv '$out_long' |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
9 && |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
10 cp annotation_overlap.csv '$out_wide' |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
11 |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
12 ]]></command> |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
13 <inputs> |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
14 <param type="data" name="input1_gff" format="gff" label="First GFF"> |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
15 <sanitizer invalid_char=""> |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
16 <valid initial="string.ascii_letters,string.digits"> |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
17 <add value="_" /> |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
18 </valid> |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
19 </sanitizer> |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
20 </param> |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
21 <param type="data" name="input2_gff" format="gff" label="Second GFF"> |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
22 <sanitizer invalid_char=""> |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
23 <valid initial="string.ascii_letters,string.digits"> |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
24 <add value="_" /> |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
25 </valid> |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
26 </sanitizer> |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
27 </param> |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
28 <param type="text" name="attribute_name" label="Name of attribute to summarize"/> |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
29 </inputs> |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
30 <outputs> |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
31 <data name="out_long" format="tabular" label="Overlap of annotations |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
32 ${input1_gff.hid} and ${input1_gff.hid} (as matrix)" /> |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
33 <data name="out_wide" format="tabular" label="Overlap of annotations |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
34 ${input1_gff.hid} and ${input1_gff.hid} (as table)"/> |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
35 </outputs> |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
36 <help><![CDATA[ |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
37 Compare overlaps in two GFF3 by selected attribute. Overlap is reported a number of bases. It expects not overlap within individuals GFF3. |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
38 ]]></help> |
b53f5a456d01
"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
petr-novak
parents:
diff
changeset
|
39 </tool> |