Mercurial > repos > petr-novak > dante_ltr

annotate README.md @ 5:0c3111ab729b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 5a81f1734493a3acf5ff24a573fa2887d92b58a8"
author petr-novak
date Mon, 16 May 2022 07:50:41 +0000
parents 7b0bbe7477c4
children 9de392f2fc02
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
1 # dante_ltr
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
2
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
3 Tool for identification of complete LTR retrotransposons based on analysis of protein
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
4 domains identified by DANTE tool.
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
5
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
6 ## Installation:
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
7
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
8 ```shell
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
9 conda create -n dante_ltr -c bioconda -c conda-forge -c petrnovak dante_ltr
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
10 ```
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
11 ## Usage
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
12
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
13 ```shell
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
14 Usage: ./extract_putative_ltr.R COMMAND [OPTIONS]
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
15
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
16
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
17 Options:
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
18 -g GFF3, --gff3=GFF3
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
19 gff3 with dante results
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
20
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
21 -s REFERENCE_SEQUENCE, --reference_sequence=REFERENCE_SEQUENCE
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
22 reference sequence as fasta
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
23
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
24 -o OUTPUT, --output=OUTPUT
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
25 output file path and prefix
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
26
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
27 -c NUMBER, --cpu=NUMBER
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
28 Number of cpu to use [default 5]
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
29
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
30 -h, --help
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
31 Show this help message and exit
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
32 ```
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
33
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
34 ## Example
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
35 ```shell
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
36 mkdir -p tmp
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
37 ./extract_putative_ltr.R -g test_data/sample_DANTE.gff3 -s test_data/sample_genome.fasta -o tmp/ltr_annotation
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
38 ```
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
39
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
40 ## Output files
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
41
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
42
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
43 ### Output of script `extract_putative_ltr.R`:
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
44
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
45
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
46 - `prefix.gff3` - annotation of all identified elements
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
47 - `prefix_DL.fasta` - elements with protein **d**omains and **L**TR
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
48 - `prefix_DLTP.fasta` - elements with **d**omains, **L**TR, **T**SD and **P**BS
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
49 - `prefix_DLP.fasta` - elements with **d**omains, **L**TR and **P**BS
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
50 - `prefix_DLT.fasta` - elements with **d**omains, **L**TR, **T**SD
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
51 - `prefix_statistics.csv` - number of elements in individual categories