Mercurial > repos > petr-novak > dante_ltr
annotate dante_ltr_search.xml @ 16:7ec262f92d89 draft
planemo upload commit ba9c740b818bbd5b5a7a5e2afbea827f5bb91419
author | petr-novak |
---|---|
date | Wed, 10 May 2023 13:07:41 +0000 |
parents | 0ea5d893a057 |
children | d1c3b29b1478 |
rev | line source |
---|---|
16
7ec262f92d89
planemo upload commit ba9c740b818bbd5b5a7a5e2afbea827f5bb91419
petr-novak
parents:
15
diff
changeset
|
1 <tool id="dante_ltr_search" name="DANTE_LTR retrotransposon identification" version="0.2.2.4" python_template_version="3.5"> |
0
7b0bbe7477c4
"planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff
changeset
|
2 <requirements> |
16
7ec262f92d89
planemo upload commit ba9c740b818bbd5b5a7a5e2afbea827f5bb91419
petr-novak
parents:
15
diff
changeset
|
3 <requirement type="package" version="0.2.2.4">dante_ltr</requirement> |
14
3b3a87915ef6
"planemo upload commit 2b4592de91793d6bbe4182d4ca9ee749d361fd82-dirty"
petr-novak
parents:
13
diff
changeset
|
4 </requirements> |
0
7b0bbe7477c4
"planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff
changeset
|
5 <command detect_errors="exit_code"><![CDATA[ |
14
3b3a87915ef6
"planemo upload commit 2b4592de91793d6bbe4182d4ca9ee749d361fd82-dirty"
petr-novak
parents:
13
diff
changeset
|
6 echo \$PATH |
3b3a87915ef6
"planemo upload commit 2b4592de91793d6bbe4182d4ca9ee749d361fd82-dirty"
petr-novak
parents:
13
diff
changeset
|
7 && |
3b3a87915ef6
"planemo upload commit 2b4592de91793d6bbe4182d4ca9ee749d361fd82-dirty"
petr-novak
parents:
13
diff
changeset
|
8 dante_ltr --gff3 '$dante' |
3b3a87915ef6
"planemo upload commit 2b4592de91793d6bbe4182d4ca9ee749d361fd82-dirty"
petr-novak
parents:
13
diff
changeset
|
9 --reference_sequence '$reference' -M $max_missing --output output --cpu \${GALAXY_SLOTS:-1} |
0
7b0bbe7477c4
"planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff
changeset
|
10 && |
7b0bbe7477c4
"planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff
changeset
|
11 mv output.gff3 $te_ltr_gff |
7
c33d6583e548
"planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
6
diff
changeset
|
12 && |
c33d6583e548
"planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
6
diff
changeset
|
13 mv output_statistics.csv $statistics |
0
7b0bbe7477c4
"planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff
changeset
|
14 ]]></command> |
7b0bbe7477c4
"planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff
changeset
|
15 <inputs> |
14
3b3a87915ef6
"planemo upload commit 2b4592de91793d6bbe4182d4ca9ee749d361fd82-dirty"
petr-novak
parents:
13
diff
changeset
|
16 <param type="data" name="dante" format="gff3" label="GFF3 output from DANTE pipeline - full output"/> |
0
7b0bbe7477c4
"planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff
changeset
|
17 <param type="data" name="reference" format="fasta" label="Reference sequence matching DANTE output" /> |
7
c33d6583e548
"planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
6
diff
changeset
|
18 <param type="integer" name="max_missing" min="0" max="3" value="1" label="Maximum number of missing protein domains to tolerate in full length retrotransposon" /> |
0
7b0bbe7477c4
"planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff
changeset
|
19 </inputs> |
7b0bbe7477c4
"planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff
changeset
|
20 <outputs> |
6
b91ca438a1cb
"planemo upload commit 9633fb98932151f059ce02a0ce202a4374ef8d68"
petr-novak
parents:
3
diff
changeset
|
21 <data name="te_ltr_gff" format="gff3" label="LTR retrotransposons annotation (GFF3) |
b91ca438a1cb
"planemo upload commit 9633fb98932151f059ce02a0ce202a4374ef8d68"
petr-novak
parents:
3
diff
changeset
|
22 based on DANTE annotation $dante.hid and reference $reference.hid" /> |
7
c33d6583e548
"planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
6
diff
changeset
|
23 <data name="statistics" format="tabular" label="LTR retrotransposons detection |
c33d6583e548
"planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
6
diff
changeset
|
24 summary based on $dante.hid and reference $reference.hid" /> |
0
7b0bbe7477c4
"planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff
changeset
|
25 </outputs> |
7b0bbe7477c4
"planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff
changeset
|
26 <help><![CDATA[ |
7b0bbe7477c4
"planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff
changeset
|
27 This tool uses output from DANTE annotation pipeline to identify full length LTR |
7b0bbe7477c4
"planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff
changeset
|
28 transposable elements. Output is in the GFF3 format and include annotation of |
7
c33d6583e548
"planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
6
diff
changeset
|
29 5' and 3' Long Terminal Repeats, Target Site Duplication (TSD) and primer binding site (PBS). |
c33d6583e548
"planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
6
diff
changeset
|
30 |
c33d6583e548
"planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
6
diff
changeset
|
31 All identified elements contains set of protein domains as defined in |
12
ff01d4263391
"planemo upload commit 414119ad7c44562d2e956b765e97ca113bc35b2b-dirty"
petr-novak
parents:
8
diff
changeset
|
32 REXdb_. Based on the results of detection of structural features, |
7
c33d6583e548
"planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
6
diff
changeset
|
33 elements falls into five categories: |
0
7b0bbe7477c4
"planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff
changeset
|
34 |
7
c33d6583e548
"planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
6
diff
changeset
|
35 - elements with domains, 5'LTR, 3'LTR, TSD and PBS - rank DLTP |
c33d6583e548
"planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
6
diff
changeset
|
36 - elements with domains, 5'LTR, 3'LTR and PBS (TSD was not found) rank DLP |
c33d6583e548
"planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
6
diff
changeset
|
37 - elements with domains, 5' LTR, 3'LTR, TSD (PBS was not found) - rank DTL |
c33d6583e548
"planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
6
diff
changeset
|
38 - elements with protein domains, 5'LTR and 3'LTR (PBS and LDS were not found) - rank DL |
c33d6583e548
"planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents:
6
diff
changeset
|
39 - elements as cluster of proteins domains with same classification, no LTRs - rank D |
0
7b0bbe7477c4
"planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff
changeset
|
40 |
7b0bbe7477c4
"planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff
changeset
|
41 .. _REXdb: https://doi.org/10.1186/s13100-018-0144-1 |
7b0bbe7477c4
"planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff
changeset
|
42 |
12
ff01d4263391
"planemo upload commit 414119ad7c44562d2e956b765e97ca113bc35b2b-dirty"
petr-novak
parents:
8
diff
changeset
|
43 Principles of detection of LTR retrotransposons is describet in github_ repository of this tool. |
ff01d4263391
"planemo upload commit 414119ad7c44562d2e956b765e97ca113bc35b2b-dirty"
petr-novak
parents:
8
diff
changeset
|
44 |
ff01d4263391
"planemo upload commit 414119ad7c44562d2e956b765e97ca113bc35b2b-dirty"
petr-novak
parents:
8
diff
changeset
|
45 .. _github: https://github.com/kavonrtep/dante_ltr |
ff01d4263391
"planemo upload commit 414119ad7c44562d2e956b765e97ca113bc35b2b-dirty"
petr-novak
parents:
8
diff
changeset
|
46 |
ff01d4263391
"planemo upload commit 414119ad7c44562d2e956b765e97ca113bc35b2b-dirty"
petr-novak
parents:
8
diff
changeset
|
47 |
0
7b0bbe7477c4
"planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff
changeset
|
48 ]]></help> |
7b0bbe7477c4
"planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff
changeset
|
49 </tool> |