Mercurial > repos > petr-novak > dante_ltr

annotate dante_ltr_search.xml @ 24:e61f06df42b9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 90a125a687a7013e6f00b057db670db5583c3b0f
author petr-novak
date Thu, 18 Apr 2024 08:56:19 +0000
parents d5508ce50c49
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
17
d1c3b29b1478 planemo upload commit ce025ba66edc87ff8ced32d5fdb36109f12cebf0-dirty
petr-novak
parents: 16
diff changeset
1 <tool id="dante_ltr_search" name="DANTE_LTR retrotransposon identification" version="@TOOL_VERSION@" python_template_version="3.5">
d1c3b29b1478 planemo upload commit ce025ba66edc87ff8ced32d5fdb36109f12cebf0-dirty
petr-novak
parents: 16
diff changeset
2 <macros>
d1c3b29b1478 planemo upload commit ce025ba66edc87ff8ced32d5fdb36109f12cebf0-dirty
petr-novak
parents: 16
diff changeset
3 <import>macros.xml</import>
d1c3b29b1478 planemo upload commit ce025ba66edc87ff8ced32d5fdb36109f12cebf0-dirty
petr-novak
parents: 16
diff changeset
4 </macros>
d1c3b29b1478 planemo upload commit ce025ba66edc87ff8ced32d5fdb36109f12cebf0-dirty
petr-novak
parents: 16
diff changeset
5 <expand macro="requirements" />
0
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
6 <command detect_errors="exit_code"><![CDATA[
14
3b3a87915ef6 "planemo upload commit 2b4592de91793d6bbe4182d4ca9ee749d361fd82-dirty"
petr-novak
parents: 13
diff changeset
7 echo \$PATH
3b3a87915ef6 "planemo upload commit 2b4592de91793d6bbe4182d4ca9ee749d361fd82-dirty"
petr-novak
parents: 13
diff changeset
8 &&
3b3a87915ef6 "planemo upload commit 2b4592de91793d6bbe4182d4ca9ee749d361fd82-dirty"
petr-novak
parents: 13
diff changeset
9 dante_ltr --gff3 '$dante'
3b3a87915ef6 "planemo upload commit 2b4592de91793d6bbe4182d4ca9ee749d361fd82-dirty"
petr-novak
parents: 13
diff changeset
10 --reference_sequence '$reference' -M $max_missing --output output --cpu \${GALAXY_SLOTS:-1}
0
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
11 &&
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
12 mv output.gff3 $te_ltr_gff
7
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents: 6
diff changeset
13 &&
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents: 6
diff changeset
14 mv output_statistics.csv $statistics
22
d5508ce50c49 planemo upload commit 398baa926d7864efeb2c349c52827fd6988e60e6-dirty
petr-novak
parents: 17
diff changeset
15 &&
d5508ce50c49 planemo upload commit 398baa926d7864efeb2c349c52827fd6988e60e6-dirty
petr-novak
parents: 17
diff changeset
16 if [ -f output_summary.html ]; then cp output_summary.html $html_report; fi
d5508ce50c49 planemo upload commit 398baa926d7864efeb2c349c52827fd6988e60e6-dirty
petr-novak
parents: 17
diff changeset
17 &&
d5508ce50c49 planemo upload commit 398baa926d7864efeb2c349c52827fd6988e60e6-dirty
petr-novak
parents: 17
diff changeset
18 mkdir -p ${html_report.extra_files_path}
d5508ce50c49 planemo upload commit 398baa926d7864efeb2c349c52827fd6988e60e6-dirty
petr-novak
parents: 17
diff changeset
19 &&
d5508ce50c49 planemo upload commit 398baa926d7864efeb2c349c52827fd6988e60e6-dirty
petr-novak
parents: 17
diff changeset
20 if [ -d output_summary_plots ]; then cp -r output_summary_plots ${html_report.extra_files_path}/; fi
0
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
21 ]]></command>
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
22 <inputs>
14
3b3a87915ef6 "planemo upload commit 2b4592de91793d6bbe4182d4ca9ee749d361fd82-dirty"
petr-novak
parents: 13
diff changeset
23 <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
24 <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
25 <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
26 </inputs>
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
27 <outputs>
6
b91ca438a1cb "planemo upload commit 9633fb98932151f059ce02a0ce202a4374ef8d68"
petr-novak
parents: 3
diff changeset
28 <data name="te_ltr_gff" format="gff3" label="LTR retrotransposons annotation (GFF3)
b91ca438a1cb "planemo upload commit 9633fb98932151f059ce02a0ce202a4374ef8d68"
petr-novak
parents: 3
diff changeset
29 based on DANTE annotation $dante.hid and reference $reference.hid" />
7
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents: 6
diff changeset
30 <data name="statistics" format="tabular" label="LTR retrotransposons detection
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents: 6
diff changeset
31 summary based on $dante.hid and reference $reference.hid" />
22
d5508ce50c49 planemo upload commit 398baa926d7864efeb2c349c52827fd6988e60e6-dirty
petr-novak
parents: 17
diff changeset
32 <data name="html_report" format="html" label="LTR retrotransposons detection on $dante.hid and $reference.hid report" />
d5508ce50c49 planemo upload commit 398baa926d7864efeb2c349c52827fd6988e60e6-dirty
petr-novak
parents: 17
diff changeset
33
0
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
34 </outputs>
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
35 <help><![CDATA[
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
36 This tool uses output from DANTE annotation pipeline to identify full length LTR
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
37 transposable elements. Output is in the GFF3 format and include annotation of
7
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents: 6
diff changeset
38 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
39
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents: 6
diff changeset
40 All identified elements contains set of protein domains as defined in
12
ff01d4263391 "planemo upload commit 414119ad7c44562d2e956b765e97ca113bc35b2b-dirty"
petr-novak
parents: 8
diff changeset
41 REXdb_. Based on the results of detection of structural features,
7
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents: 6
diff changeset
42 elements falls into five categories:
0
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
43
7
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents: 6
diff changeset
44 - elements with domains, 5'LTR, 3'LTR, TSD and PBS - rank DLTP
c33d6583e548 "planemo upload commit 50884f7f0269a0bbde078f24fe5020975693bcd9"
petr-novak
parents: 6
diff changeset
45 - 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
46 - 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
47 - 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
48 - 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
49
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
50 .. _REXdb: https://doi.org/10.1186/s13100-018-0144-1
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
51
12
ff01d4263391 "planemo upload commit 414119ad7c44562d2e956b765e97ca113bc35b2b-dirty"
petr-novak
parents: 8
diff changeset
52 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
53
ff01d4263391 "planemo upload commit 414119ad7c44562d2e956b765e97ca113bc35b2b-dirty"
petr-novak
parents: 8
diff changeset
54 .. _github: https://github.com/kavonrtep/dante_ltr
ff01d4263391 "planemo upload commit 414119ad7c44562d2e956b765e97ca113bc35b2b-dirty"
petr-novak
parents: 8
diff changeset
55
ff01d4263391 "planemo upload commit 414119ad7c44562d2e956b765e97ca113bc35b2b-dirty"
petr-novak
parents: 8
diff changeset
56
0
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
57 ]]></help>
7b0bbe7477c4 "planemo upload commit 92c684dff3b377c8c08654c7f3d46a133385e3e0-dirty"
petr-novak
parents:
diff changeset
58 </tool>