annotate ChipSeqRatioDef.xml @ 17:d14b68e9fd1d draft

Uploaded - new tools added
author petr-novak
date Wed, 28 Apr 2021 08:37:20 +0000
parents 5376e1c9adec
children 58807b35777a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
16
5376e1c9adec Uploaded
petr-novak
parents: 9
diff changeset
1 <tool id="chip_seq_ratio_1" name="ChIP-Seq Mapper" version="0.1.1">
3
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
2 <stdio>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
3 <exit_code range="1:" level="fatal" description="Error"/>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
4 </stdio>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
5 <description></description>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
6 <requirements>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
7 <requirement type="package">r-base64enc</requirement>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
8 <requirement type="package">r-r2html</requirement>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
9 <requirement type="package">blast</requirement>
6
f224513123a1 Uploaded
petr-novak
parents: 3
diff changeset
10 <!-- <requirement type="package">chip_seq_ration</requirement> -->
3
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
11 </requirements>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
12 <command interpreter="python3">
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
13 ChipSeqRatioAnalysis.py
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
14 --ChipSeq=${ChipFile}
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
15 --InputSeq=${InputFile}
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
16 --Contigs=${ContigFile}
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
17 --output=${OutputFile}
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
18 --html=${ReportFile}
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
19 --max_cl=${MaxCl}
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
20 --bitscore=$bitscore
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
21 --nproc=16
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
22 </command>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
23
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
24 <inputs>
9
c2c69c6090f0 Uploaded
petr-novak
parents: 7
diff changeset
25 <param name="ChipFile" label="Chip reads" type="data" format="fasta" help="Reads in FASTA format"/>
c2c69c6090f0 Uploaded
petr-novak
parents: 7
diff changeset
26 <param name="InputFile" label="Input reads" type="data" format="fasta" help="Reads in FASTA format"/>
c2c69c6090f0 Uploaded
petr-novak
parents: 7
diff changeset
27 <param name="ContigFile" label="Reference - contig sequences" type="data" format="fasta"
c2c69c6090f0 Uploaded
petr-novak
parents: 7
diff changeset
28 help="Contigs from RepeatExplorer clustering (the file &quot;contigs.fasta&quot;)"/>
c2c69c6090f0 Uploaded
petr-novak
parents: 7
diff changeset
29 <param name="MaxCl" label="Number of top clusters to be shown in graph" type="integer" value="200"/>
c2c69c6090f0 Uploaded
petr-novak
parents: 7
diff changeset
30 <param name="bitscore" label="Bit score threshold" type="integer" value="50" help="Similarity hits with lower bit score will not be used for ChIP/Input ratio calculation"/>
3
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
31 </inputs>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
32 <outputs>
7
89c5ba120b21 Uploaded
petr-novak
parents: 6
diff changeset
33 <data name="OutputFile" format="tabular"
89c5ba120b21 Uploaded
petr-novak
parents: 6
diff changeset
34 label="csv table from ChIP-Seq-Mapper on datasets ${InputFile.hid} (Input) ${ChipFile.hid} (ChIP) and ${ContigFile.hid} (reference)"/>
89c5ba120b21 Uploaded
petr-novak
parents: 6
diff changeset
35
89c5ba120b21 Uploaded
petr-novak
parents: 6
diff changeset
36 <data name="ReportFile" format="html"
89c5ba120b21 Uploaded
petr-novak
parents: 6
diff changeset
37 label="HTML report from ChIP-Seq-Mapper on datasets ${InputFile.hid} (Input) ${ChipFile.hid} (ChIP) and ${ContigFile.hid} (reference)"/>
3
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
38 </outputs>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
39
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
40 <help>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
41 **What it does**
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
42
9
c2c69c6090f0 Uploaded
petr-novak
parents: 7
diff changeset
43 The ChIP-seq Mapper evaluates the enrichment of repetitive sequences in sequencing data from chromatin
c2c69c6090f0 Uploaded
petr-novak
parents: 7
diff changeset
44 immunoprecipitation experiments, using repeats identified by RepeatExplorer as the reference. The tool
c2c69c6090f0 Uploaded
petr-novak
parents: 7
diff changeset
45 performs BLASTN similarity search of the read sequences to the reference,
c2c69c6090f0 Uploaded
petr-novak
parents: 7
diff changeset
46 and the reads producing hits that passed the user-specified similarity threshold are assigned to the
c2c69c6090f0 Uploaded
petr-novak
parents: 7
diff changeset
47 repeat clusters. The assignment is made to the cluster that produced the best similarity hit, and every
c2c69c6090f0 Uploaded
petr-novak
parents: 7
diff changeset
48 read is assigned to only a single cluster. Following read mapping, the numbers of reads from the
c2c69c6090f0 Uploaded
petr-novak
parents: 7
diff changeset
49 INPUT and ChIP samples are evaluated, and ChIP/INPUT ratios of the normalized read counts are reported
c2c69c6090f0 Uploaded
petr-novak
parents: 7
diff changeset
50 for individual clusters.
c2c69c6090f0 Uploaded
petr-novak
parents: 7
diff changeset
51 ChIP and INPUT reads should be of uniform lengths of at least 40 nt. The bit score threshold value should be
c2c69c6090f0 Uploaded
petr-novak
parents: 7
diff changeset
52 adjusted based on the length of the analyzed reads (the value equal to the read length is recommended for a start).
3
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
53 This method was first used in (`Neumann et al. 2012`__) for
9
c2c69c6090f0 Uploaded
petr-novak
parents: 7
diff changeset
54 identification of repetitive sequences associated with centromeres:
3
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
55
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
56
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
57 `PLoS Genet. Epub 2012 Jun 21. Stretching the rules: monocentric chromosomes with multiple centromere domains. Neumann P, Navrátilová A, Schroeder-Reiter E, Koblížková A, Steinbauerová V, Chocholová E, Novák P, Wanner G, Macas J.`__.
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
58
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
59 .. __: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002777
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
60 .. __: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002777
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
61
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
62 </help>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
63
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
64 </tool>
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
65
e320ef2d105a Uploaded
petr-novak
parents:
diff changeset
66