Mercurial > repos > petr-novak > dante_ltr

annotate dante_ltr_search.xml @ 14:3b3a87915ef6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2b4592de91793d6bbe4182d4ca9ee749d361fd82-dirty"
author petr-novak
date Mon, 30 Jan 2023 10:05:47 +0000
parents 559940c04c44
children 0ea5d893a057
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
14
3b3a87915ef6 "planemo upload commit 2b4592de91793d6bbe4182d4ca9ee749d361fd82-dirty"
petr-novak
parents: 13
diff changeset
1 <tool id="dante_ltr_search" name="DANTE_LTR retrotransposon identification" version="0.2.2.0" python_template_version="3.5">
0
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
2 <requirements>
14
3b3a87915ef6 "planemo upload commit 2b4592de91793d6bbe4182d4ca9ee749d361fd82-dirty"
petr-novak
parents: 13
diff changeset
3 <requirement type="package">dante_ltr=0.2.2.0</requirement>
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>