Mercurial > repos > petrn > repeat_annotation_pipeline

annotate format_repeat_library.xml @ 0:d14182506989 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
author petrn
date Tue, 15 Feb 2022 16:44:31 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
1 <tool id="annotate_contigs" name="Format Repeat Library" version="0.1.0" python_template_version="3.5">
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
2 <requirements>
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
3 <requirement type="package" version="2.60.0">bioconductor-biostrings</requirement>
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
4 </requirements>
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
5 <command detect_errors="exit_code"><![CDATA[
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
6 $__tool_directory__/annotate_contigs.R '$contigs' '$cluster_table' '$annotated_contigs'
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
7 ]]></command>
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
8 <inputs>
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
9 <param type="data" name="contigs" format="fasta" label="Contigs - Library of Repeats from TAREAN/RepeatExplorer pipeline" />
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
10 <param type="data" name="cluster_table" format="txt" label="CLUSTER_TABLE from RepeatExplorer pipeline" help="CLUSTER_TABLE which contain annotation of clusters from RepeatExplorer pipeline"/>
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
11 </inputs>
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
12 <outputs>
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
13 <data name="annotated_contigs" format="fasta" label="Annotated Repeat Library based on ${contigs.hid} and ${cluster_table.hid}" />
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
14 </outputs>
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
15 <help><![CDATA[
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
16 **What this tool does**
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
17
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
18 Contigs from RepeatExplorer archive are annotated based on the classification of repeats from cluster_table.
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
19
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
20 Preformated CLUSTER_TABLE can be extracted from RepeatExplorer archive and modified accordingly. By default, "Final_annotation" column is used to append annotation to contigs in repeat library (based on the cluster id). If "Final_annotation" column is incomplete, "Automatic_annotation" column is used instead.
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
21
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
22 Example of tab delimited CLUSTER_TABLE::
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
23
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
24
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
25 "Number_of_reads_in_clusters" 3886
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
26 "Number_of_clusters" 822
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
27 "Number_of_superclusters" 821
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
28 "Number_of_singlets" 6114
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
29 "Number_of_analyzed_reads" 10000
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
30
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
31 "Cluster" "Supercluster" "Size" "Size_adjusted" "Automatic_annotation" "TAREAN_annotation" "Final_annotation"
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
32 1 1 260 260 "All/repeat/satellite" "Putative satellites (low confidence)" ""
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
33 2 2 157 157 "All/repeat/satellite" "Putative satellites (low confidence)" ""
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
34 3 4 100 100 "All" "Other" ""
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
35 4 5 83 83 "All" "Other" ""
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
36 5 3 77 77 "All" "Other" ""
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
37 6 3 65 65 "All" "Other" ""
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
38 7 6 61 61 "All" "Other" ""
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
39 8 7 58 58 "All" "Other" ""
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
40 9 8 53 53 "All" "Other" ""
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
41 10 9 53 53 "All" "Other" ""
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
42 11 10 51 51 "All" "Other" ""
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
43 12 11 45 45 "All" "Other" ""
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
44 13 12 44 44 "All" "Other" ""
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
45 14 13 44 44 "All" "Other" ""
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
46 15 14 39 39 "All" "Other" ""
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
47 16 15 37 37 "All" "Other" ""
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
48 17 16 30 30 "All/repeat/satellite" "Putative satellites (low confidence)" ""
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
49 18 17 28 28 "All/repeat/satellite" "Putative satellites (low confidence)" ""
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
50 19 18 26 26 "All/repeat/satellite" "Putative satellites (high confidence)" ""
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
51 20 19 23 23 "All/repeat/../CRM" "Other" ""
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
52 21 20 21 21 "All" "Other" ""
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
53 22 21 21 21 "All" "Other" ""
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
54 23 22 21 21 "All" "Other" ""
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
55 24 23 21 21 "All" "Other" ""
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
56 25 24 20 20 "All/repeat/../Ogre" "Other" ""
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
57
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
58
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
59 Only Cluster, Automatic_annotation/Final_annnotation are mandatory"
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
60
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
61 Clusters with higher number than those in CLUSTER_TABLE are removed from Repeat library
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
62
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
63 Contigs are provided in followinf format::
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
64
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
65
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
66 >CL25Contig1
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
67 AGATCAAGATGGCGCCGGAGGACATGGAGAAAACGACGTTTATCACTCCCTGGGGAACATTTTGCTACAAGGTAATGCCT
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
68 TTCGGTCTGAAGAACGCAGGGGCCACTTACCAACGAGCAATGGTAACTT
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
69 >CL1Contig4#All/repeat/satellite
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
70 ACCCGAAGGCCGGCTCAACCCGAAGTTGAGAAGAACATCTGACCTCGCCGTCAGGCATCTGTTAAACAAACAGGCATCGA
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
71 A
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
72 >CL1Contig5
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
73 TGAGAAGAACATCTGACCTCGCCGTCAGGCATCTGTTAAACAAACAGGCATCGAACCCGAAGGCCGGCTCAACCCGAAGT
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
74 TGATAAGAACATCTGACCTCGCCGTCAGGCATCTGTTAAACAAACAGGCATCGAACCCGAAGGCCGGCTCAACACGAAGT
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
75 TGAGAGGAACATCTGACCTCGCCGTCAGGCATCTGTTAAA
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
76
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
77
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
78 Resulting repeat library will have following format::
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
79
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
80 >CL25Contig1#All/repeat/mobile_element/Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Tat/Ogre
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
81 AGATCAAGATGGCGCCGGAGGACATGGAGAAAACGACGTTTATCACTCCCTGGGGAACATTTTGCTACAAGGTAATGCCT
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
82 TTCGGTCTGAAGAACGCAGGGGCCACTTACCAACGAGCAATGGTAACTT
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
83 >CL1Contig4#All/repeat/satellite
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
84 ACCCGAAGGCCGGCTCAACCCGAAGTTGAGAAGAACATCTGACCTCGCCGTCAGGCATCTGTTAAACAAACAGGCATCGA
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
85 A
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
86 >CL1Contig5#All/repeat/satellite
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
87 TGAGAAGAACATCTGACCTCGCCGTCAGGCATCTGTTAAACAAACAGGCATCGAACCCGAAGGCCGGCTCAACCCGAAGT
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
88 TGATAAGAACATCTGACCTCGCCGTCAGGCATCTGTTAAACAAACAGGCATCGAACCCGAAGGCCGGCTCAACACGAAGT
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
89 TGAGAGGAACATCTGACCTCGCCGTCAGGCATCTGTTAAA
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
90
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
91
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
92
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
93
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
94 ]]></help>
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
parents:
diff changeset
95 </tool>