Mercurial > repos > petr-novak > re_utils

annotate summarize_cluster_table.xml @ 27:eefed7a82001 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
author petr-novak
date Wed, 02 Aug 2023 12:59:29 +0000
parents 58807b35777a
children 628b235d76c7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
22
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
1 <tool id="summarize_annotation" name="Repeat proportions from CLUSTER_TABLE"
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
2 version="1.0.0.3">
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
3 <description>Simple utility to summarize final annotations from RepeatExplorer
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
4 CLUSTER_TABLE
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
5 </description>
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
6 <requirements>
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
7 <requirement type="package">r-optparse</requirement>
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
8 </requirements>
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
9 <required_files>
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
10 <include type="literal" path="summarize_cluster_table.R"/>
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
11 </required_files>
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
12 <command interpreter="Rscript" detect_errors="exit_code">
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
13 Rscript $__tool_directory__/summarize_cluster_table.R
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
14 --cluster_table=$cluster_table
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
15 --output=$output
18
d7f3eff34c27 Uploaded
petr-novak
parents:
diff changeset
16
d7f3eff34c27 Uploaded
petr-novak
parents:
diff changeset
17 </command>
d7f3eff34c27 Uploaded
petr-novak
parents:
diff changeset
18
d7f3eff34c27 Uploaded
petr-novak
parents:
diff changeset
19 <inputs>
22
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
20 <param format="txt" type="data" name="cluster_table"
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
21 label="file from RepeatExplorer2 clustering - CLUSTER_TABLE.csv"
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
22 help="CLUSTER_TABLE.csv must contains completed Final_annotation column"/>
18
d7f3eff34c27 Uploaded
petr-novak
parents:
diff changeset
23 </inputs>
d7f3eff34c27 Uploaded
petr-novak
parents:
diff changeset
24
d7f3eff34c27 Uploaded
petr-novak
parents:
diff changeset
25 <outputs>
22
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
26 <data format="tabular" name="output"
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
27 label="Summary of repeat proportions from ${cluster_table.hid}"/>
18
d7f3eff34c27 Uploaded
petr-novak
parents:
diff changeset
28 </outputs>
d7f3eff34c27 Uploaded
petr-novak
parents:
diff changeset
29 <help>
22
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
30 **The tool calculates genome proportions of identified repeats based on cluster
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
31 annotations in CLUSTER_TABLE.csv**
18
d7f3eff34c27 Uploaded
petr-novak
parents:
diff changeset
32
22
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
33 The column "Final_annotation" must be filled in the input file CLUSTER_TABLE.csv.
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
34 Contamination and organelle clusters are discarded from quantification. Table
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
35 header with information about numbers of analyzed reads should remain unchanged -
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
36 see example below.
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
37
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
38 Example of CLUSTER_TABLE.csv: ::
18
d7f3eff34c27 Uploaded
petr-novak
parents:
diff changeset
39
22
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
40 Number_of_reads_in_clusters 1185180
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
41 Number_of_clusters 62148
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
42 Number_of_superclusters 62031
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
43 Number_of_singlets 314820
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
44 Number_of_analyzed_reads 1500000
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
45 Cluster Supercluster Size Size_adjusted Automatic_annotation TAREAN_annotation
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
46 Final_annotation
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
47 10 4 11967 11967 All/repeat/mobile_element/Class_I/LTR/Ty1_copia/SIRE Other
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
48 All/repeat/mobile_element/Class_I/LTR/Ty1_copia/SIRE
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
49 137 5 2094 2094 All/repeat Other All/repeat
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
50 112 9 3117 3117 All/repeat/rDNA/45S_rDNA Other All/repeat/rDNA/45S_rDNA
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
51 16 11 10078 10078 All/repeat/satellite Putative satellites (high confidence)
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
52 All/repeat/satellite
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
53 125 22 2630 2630 All/organelle/plastid Other All/organelle/plastid
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
54 124 40 2645 2645 All/repeat/mobile_element/Class_I/LTR/Ty1_copia/Ivana Putative
58807b35777a planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents: 19
diff changeset
55 LTR elements All/repeat/mobile_element/Class_I/LTR/Ty1_copia/Ivana
18
d7f3eff34c27 Uploaded
petr-novak
parents:
diff changeset
56
d7f3eff34c27 Uploaded
petr-novak
parents:
diff changeset
57 </help>
d7f3eff34c27 Uploaded
petr-novak
parents:
diff changeset
58 </tool>