Mercurial > repos > petr-novak > re_utils
changeset 29:53dc6aef5441 draft
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
| author | petr-novak |
|---|---|
| date | Thu, 03 Aug 2023 07:32:40 +0000 |
| parents | ba970b24e48c |
| children | cab41d23e2a3 |
| files | ChipSeqRatioDef.xml |
| diffstat | 1 files changed, 58 insertions(+), 38 deletions(-) [+] |
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--- a/ChipSeqRatioDef.xml Wed Aug 02 13:09:47 2023 +0000 +++ b/ChipSeqRatioDef.xml Thu Aug 03 07:32:40 2023 +0000 @@ -1,19 +1,21 @@ -<tool id="chip_seq_ratio_1" name="ChIP-Seq Mapper" version="1.1.1.3"> - <stdio> - <exit_code range="1:" level="fatal" description="Error"/> - </stdio> +<tool id="chip_seq_ratio_1" name="ChIP-Seq Mapper" version="1.1.1.4"> + <stdio> + <exit_code range="1:" level="fatal" description="Error"/> + </stdio> <description></description> <requirements> - <requirement type="package">r-base64enc</requirement> - <requirement type="package">r-r2html</requirement> - <requirement type="package">blast</requirement> - <!-- <requirement type="package">chip_seq_ration</requirement> --> + <requirement type="package">r-base64enc</requirement> + <requirement type="package">r-r2html</requirement> + <requirement type="package">blast</requirement> + <requirement type="package" version="3">python</requirement> + <!-- <requirement type="package">chip_seq_ration</requirement> --> </requirements> <required_files> <include type="literal" path="ChipSeqRatioAnalysis.py"/> <include type="literal" path="ChipSeqRatioAnalysis.R"/> </required_files> - <command> + <command> <![CDATA[ + which python && python --version && python '$__tool_directory__'/ChipSeqRatioAnalysis.py --ChipSeq=${ChipFile} --InputSeq=${InputFile} @@ -21,48 +23,66 @@ --output=${OutputFile} --html=${ReportFile} --max_cl=${MaxCl} - --bitscore=$bitscore - --nproc=16 + --bitscore=$bitscore + --nproc=16 + ]]> </command> <inputs> - <param name="ChipFile" label="Chip reads" type="data" format="fasta" help="Reads in FASTA format"/> - <param name="InputFile" label="Input reads" type="data" format="fasta" help="Reads in FASTA format"/> - <param name="ContigFile" label="Reference - contig sequences" type="data" format="fasta" - help="Contigs from RepeatExplorer clustering (the file "contigs.fasta")"/> - <param name="MaxCl" label="Number of top clusters to be shown in graph" type="integer" value="200"/> - <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"/> + <param name="ChipFile" label="Chip reads" type="data" format="fasta" + help="Reads in FASTA format"/> + <param name="InputFile" label="Input reads" type="data" format="fasta" + help="Reads in FASTA format"/> + <param name="ContigFile" label="Reference - contig sequences" type="data" + format="fasta" + help="Contigs from RepeatExplorer clustering (the file "contigs.fasta")"/> + <param name="MaxCl" label="Number of top clusters to be shown in graph" + type="integer" value="200"/> + <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"/> </inputs> <outputs> - <data name="OutputFile" format="tabular" - label="csv table from ChIP-Seq-Mapper on datasets ${InputFile.hid} (Input) ${ChipFile.hid} (ChIP) and ${ContigFile.hid} (reference)"/> + <data name="OutputFile" format="tabular" + label="csv table from ChIP-Seq-Mapper on datasets ${InputFile.hid} (Input) ${ChipFile.hid} (ChIP) and ${ContigFile.hid} (reference)"/> - <data name="ReportFile" format="html" - label="HTML report from ChIP-Seq-Mapper on datasets ${InputFile.hid} (Input) ${ChipFile.hid} (ChIP) and ${ContigFile.hid} (reference)"/> + <data name="ReportFile" format="html" + label="HTML report from ChIP-Seq-Mapper on datasets ${InputFile.hid} (Input) ${ChipFile.hid} (ChIP) and ${ContigFile.hid} (reference)"/> </outputs> <help> -**What it does** + **What it does** -The ChIP-seq Mapper evaluates the enrichment of repetitive sequences in sequencing data from chromatin -immunoprecipitation experiments, using repeats identified by RepeatExplorer as the reference. The tool -performs BLASTN similarity search of the read sequences to the reference, -and the reads producing hits that passed the user-specified similarity threshold are assigned to the -repeat clusters. The assignment is made to the cluster that produced the best similarity hit, and every -read is assigned to only a single cluster. Following read mapping, the numbers of reads from the -INPUT and ChIP samples are evaluated, and ChIP/INPUT ratios of the normalized read counts are reported -for individual clusters. -ChIP and INPUT reads should be of uniform lengths of at least 40 nt. The bit score threshold value should be -adjusted based on the length of the analyzed reads (the value equal to the read length is recommended for a start). -This method was first used in (`Neumann et al. 2012`__) for -identification of repetitive sequences associated with centromeres: + The ChIP-seq Mapper evaluates the enrichment of repetitive sequences in sequencing + data from chromatin + immunoprecipitation experiments, using repeats identified by RepeatExplorer as the + reference. The tool + performs BLASTN similarity search of the read sequences to the reference, + and the reads producing hits that passed the user-specified similarity threshold + are assigned to the + repeat clusters. The assignment is made to the cluster that produced the best + similarity hit, and every + read is assigned to only a single cluster. Following read mapping, the numbers of + reads from the + INPUT and ChIP samples are evaluated, and ChIP/INPUT ratios of the normalized read + counts are reported + for individual clusters. + ChIP and INPUT reads should be of uniform lengths of at least 40 nt. The bit score + threshold value should be + adjusted based on the length of the analyzed reads (the value equal to the read + length is recommended for a start). + This method was first used in (`Neumann et al. 2012`__) for + identification of repetitive sequences associated with centromeres: -`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.`__. + `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.`__. -.. __: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002777 -.. __: http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002777 - + .. __: + http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002777 + .. __: + http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002777 + </help> </tool>