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comparison ChipSeqRatioDef.xml @ 29:53dc6aef5441 draft

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author petr-novak
date Thu, 03 Aug 2023 07:32:40 +0000
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28:ba970b24e48c 29:53dc6aef5441
1 <tool id="chip_seq_ratio_1" name="ChIP-Seq Mapper" version="1.1.1.3"> 1 <tool id="chip_seq_ratio_1" name="ChIP-Seq Mapper" version="1.1.1.4">
2 <stdio> 2 <stdio>
3 <exit_code range="1:" level="fatal" description="Error"/> 3 <exit_code range="1:" level="fatal" description="Error"/>
4 </stdio> 4 </stdio>
5 <description></description> 5 <description></description>
6 <requirements> 6 <requirements>
7 <requirement type="package">r-base64enc</requirement> 7 <requirement type="package">r-base64enc</requirement>
8 <requirement type="package">r-r2html</requirement> 8 <requirement type="package">r-r2html</requirement>
9 <requirement type="package">blast</requirement> 9 <requirement type="package">blast</requirement>
10 <!-- <requirement type="package">chip_seq_ration</requirement> --> 10 <requirement type="package" version="3">python</requirement>
11 <!-- <requirement type="package">chip_seq_ration</requirement> -->
11 </requirements> 12 </requirements>
12 <required_files> 13 <required_files>
13 <include type="literal" path="ChipSeqRatioAnalysis.py"/> 14 <include type="literal" path="ChipSeqRatioAnalysis.py"/>
14 <include type="literal" path="ChipSeqRatioAnalysis.R"/> 15 <include type="literal" path="ChipSeqRatioAnalysis.R"/>
15 </required_files> 16 </required_files>
16 <command> 17 <command> <![CDATA[
18 which python && python --version &&
17 python '$__tool_directory__'/ChipSeqRatioAnalysis.py 19 python '$__tool_directory__'/ChipSeqRatioAnalysis.py
18 --ChipSeq=${ChipFile} 20 --ChipSeq=${ChipFile}
19 --InputSeq=${InputFile} 21 --InputSeq=${InputFile}
20 --Contigs=${ContigFile} 22 --Contigs=${ContigFile}
21 --output=${OutputFile} 23 --output=${OutputFile}
22 --html=${ReportFile} 24 --html=${ReportFile}
23 --max_cl=${MaxCl} 25 --max_cl=${MaxCl}
24 --bitscore=$bitscore 26 --bitscore=$bitscore
25 --nproc=16 27 --nproc=16
28 ]]>
26 </command> 29 </command>
27 30
28 <inputs> 31 <inputs>
29 <param name="ChipFile" label="Chip reads" type="data" format="fasta" help="Reads in FASTA format"/> 32 <param name="ChipFile" label="Chip reads" type="data" format="fasta"
30 <param name="InputFile" label="Input reads" type="data" format="fasta" help="Reads in FASTA format"/> 33 help="Reads in FASTA format"/>
31 <param name="ContigFile" label="Reference - contig sequences" type="data" format="fasta" 34 <param name="InputFile" label="Input reads" type="data" format="fasta"
32 help="Contigs from RepeatExplorer clustering (the file &quot;contigs.fasta&quot;)"/> 35 help="Reads in FASTA format"/>
33 <param name="MaxCl" label="Number of top clusters to be shown in graph" type="integer" value="200"/> 36 <param name="ContigFile" label="Reference - contig sequences" type="data"
34 <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"/> 37 format="fasta"
38 help="Contigs from RepeatExplorer clustering (the file &quot;contigs.fasta&quot;)"/>
39 <param name="MaxCl" label="Number of top clusters to be shown in graph"
40 type="integer" value="200"/>
41 <param name="bitscore" label="Bit score threshold" type="integer" value="50"
42 help="Similarity hits with lower bit score will not be used for ChIP/Input ratio calculation"/>
35 </inputs> 43 </inputs>
36 <outputs> 44 <outputs>
37 <data name="OutputFile" format="tabular" 45 <data name="OutputFile" format="tabular"
38 label="csv table from ChIP-Seq-Mapper on datasets ${InputFile.hid} (Input) ${ChipFile.hid} (ChIP) and ${ContigFile.hid} (reference)"/> 46 label="csv table from ChIP-Seq-Mapper on datasets ${InputFile.hid} (Input) ${ChipFile.hid} (ChIP) and ${ContigFile.hid} (reference)"/>
39 47
40 <data name="ReportFile" format="html" 48 <data name="ReportFile" format="html"
41 label="HTML report from ChIP-Seq-Mapper on datasets ${InputFile.hid} (Input) ${ChipFile.hid} (ChIP) and ${ContigFile.hid} (reference)"/> 49 label="HTML report from ChIP-Seq-Mapper on datasets ${InputFile.hid} (Input) ${ChipFile.hid} (ChIP) and ${ContigFile.hid} (reference)"/>
42 </outputs> 50 </outputs>
43 51
44 <help> 52 <help>
45 **What it does** 53 **What it does**
46 54
47 The ChIP-seq Mapper evaluates the enrichment of repetitive sequences in sequencing data from chromatin 55 The ChIP-seq Mapper evaluates the enrichment of repetitive sequences in sequencing
48 immunoprecipitation experiments, using repeats identified by RepeatExplorer as the reference. The tool 56 data from chromatin
49 performs BLASTN similarity search of the read sequences to the reference, 57 immunoprecipitation experiments, using repeats identified by RepeatExplorer as the
50 and the reads producing hits that passed the user-specified similarity threshold are assigned to the 58 reference. The tool
51 repeat clusters. The assignment is made to the cluster that produced the best similarity hit, and every 59 performs BLASTN similarity search of the read sequences to the reference,
52 read is assigned to only a single cluster. Following read mapping, the numbers of reads from the 60 and the reads producing hits that passed the user-specified similarity threshold
53 INPUT and ChIP samples are evaluated, and ChIP/INPUT ratios of the normalized read counts are reported 61 are assigned to the
54 for individual clusters. 62 repeat clusters. The assignment is made to the cluster that produced the best
55 ChIP and INPUT reads should be of uniform lengths of at least 40 nt. The bit score threshold value should be 63 similarity hit, and every
56 adjusted based on the length of the analyzed reads (the value equal to the read length is recommended for a start). 64 read is assigned to only a single cluster. Following read mapping, the numbers of
57 This method was first used in (`Neumann et al. 2012`__) for 65 reads from the
58 identification of repetitive sequences associated with centromeres: 66 INPUT and ChIP samples are evaluated, and ChIP/INPUT ratios of the normalized read
67 counts are reported
68 for individual clusters.
69 ChIP and INPUT reads should be of uniform lengths of at least 40 nt. The bit score
70 threshold value should be
71 adjusted based on the length of the analyzed reads (the value equal to the read
72 length is recommended for a start).
73 This method was first used in (`Neumann et al. 2012`__) for
74 identification of repetitive sequences associated with centromeres:
59 75
60 76
61 `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.`__. 77 `PLoS Genet. Epub 2012 Jun 21. Stretching the rules: monocentric chromosomes with
78 multiple centromere domains. Neumann P, Navrátilová A, Schroeder-Reiter E,
79 Koblížková A, Steinbauerová V, Chocholová E, Novák P, Wanner G, Macas J.`__.
62 80
63 .. __: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002777 81 .. __:
64 .. __: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002777 82 http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002777
65 83 .. __:
84 http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002777
85
66 </help> 86 </help>
67 87
68 </tool> 88 </tool>
69 89
70 90