nucleosome_dynamics: nucleR.xml annotate

author	spanish_national_institue_of_bioinformatics
date	Fri, 12 Apr 2019 05:28:43 -0400
parents
children

rev	line source
2 e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	1 <tool id="nucleR" name="NucleR" version="0.1">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	2 <description>: analyze aligned BAM files from MNAse (in RData format)</description>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	3 <requirements>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	4 <requirement type="binary">docker</requirement>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	5 </requirements>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	6 <command>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	7 <![CDATA[
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	8 docker run -v $__root_dir__/database/files:$__root_dir__/database/files -v /tmp:/tmp -u `id -u`:`id -g` mmbirb/nucleosome-dynamics nucleR --input $rdata_file --output $output_gff_file --type $seq_type --width $width --minoverlap $minoverlap --dyad_length $dyad_length --hthresh $hthres --wthresh $wthres --pcKeepComp $pcKeepComp --fdrOverAmp $fdrOverAmp --trim $trim --fragmentLen $fragmentLen
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	9 #if $threshold.is == "absolute":
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	10 --thresholdValue ${threshold.thresholdValue}
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	11 #else if $threshold.is == "percentage":
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	12 --thresholdPercentage ${threshold.thresholdPercentage}
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	13 #end if
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	14 #if $chr
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	15 --chr $chr
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	16 #end if
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	17 #if $start
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	18 --start $start
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	19 #end if
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	20 #if $end
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	21 --end $end
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	22 #end if
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	23 #if $comp
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	24 --components $comp
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	25 #end if
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	26 ]]>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	27 </command>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	28 <inputs>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	29 <param name="rdata_file" type="data" format="rdata" label="Input MNase-seq/ATAC-seq reads (RData)" help="Input BAM file in RData format as generated by readBAM."/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	30 <param name="seq_type" type="select" label="Type of sequence reads">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	31 <option value="paired">Paired</option>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	32 <option value="single">Single</option>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	33 </param>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	34 <param name="width" size="4" type="integer" value="147" label="Width (bp)" help="Size of each nucleosome."/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	35 <param name="minoverlap" type="integer" value="80" label="Minimum Overlap (bp)" help="Minimum overlap between two nucleosomes for merging them."/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	36 <param name="dyad_length" type="integer" value="50" label="Dyad length (bp)" help="Lenght of the reads that should be used for nucleosome calling to define the dyad of the nucleosomes keeping the number of bases around the center of the read."/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	37 <param name="fragmentLen" type="integer" value="170" label="Fragment Length (bp)" help="Maximum fragment length allowed (bp)" optional="True" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	38 <param name="chr" type="text" value="" label="Chromosome" optional="True" help="Chromosome to consider for the analysis in the given input file."/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	39 <param name="start" type="integer" value="" label="Start" optional="True" help="Start genomic position to consider for the analysis in the given input file."/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	40 <param name="end" type="integer" value="" label="End" optional="True" help="End genomic position to consider for the analysis in the given input file."/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	41 <param name="comp" type="integer" value="1" label="Components" optional="True" help="Number of negative binomials that will be used to filter duplicated reads."/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	42 <conditional name="threshold">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	43 <param name="is" type="select" label="Background threshold" help="Minimum number of reads (Coverage) to call a nucleosome. Can be given as a percentage, or an absolute number of reads.">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	44 <option value="percentage" selected="True">use a percentage</option>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	45 <option value="absolute">use a number of reads</option>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	46 </param>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	47 <when value="absolute">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	48 <param name="thresholdValue" type="integer" value="10" label="Bakground level (reads)" help="Absolute value to filter out nucleosome calls. It is the minimum number of reads (coverage) in a nucleosome call expressed as reads per million of mapped reads."/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	49 </when>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	50 <when value="percentage">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	51 <param name="thresholdPercentage" type="float" value="35" label="Background level (%)" help="Percentile of coverage in the experiment used as threshold to filter out nucleosome calls (i.e., 25% would mean that only peaks with coverage in the 1st quantile would be considered)"/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	52 </when>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	53 </conditional>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	54 <param name="hthres" type="float" value="0.4" label="Height Threshold" help="Height threshold (between 0 and 1) to classify a nucleosome as fuzzy (class=F) or well-positioned ( class=W) according to the number of reads at the dyad. Nucleosomes below this value will be defined as fuzzy."/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	55 <param name="wthres" type="float" value="0.6" label="Width Threshold" help="Width threshold (between 0 and 1) to classify a nucleosome as fuzzy (class=F) or well-positioned (class=W) according to the dispersion of the reads around the dyad."/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	56 <param name="fdrOverAmp" type="float" value="0.05" label="fdrOverAmp" help="Threshold to filter over-amplified reads , as defined in filterDuplReads function of htSetqTools R package."/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	57 <param name="pcKeepComp" type="float" value="0.02" label="Coverage Smoothing" help="Parameter used in the smoothing when Fourier transformation is applied. Number of components to select with respect to the total size of the sample. Allowed values are numeric (in range 0:1) for manual setting, or auto for automatic detection."/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	58 <param name="trim" type="integer" value="50" label="Trim" help="Number of basepairs to keep from each read (or to extend in case it is larger than the read width)."/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	59 </inputs>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	60 <outputs>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	61 <data format="gff" name="output_gff_file" label="NR__${os.path.splitext(($rdata_file.name.split('__'))[1])[0]}.gff" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	62 </outputs>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	63 <tests>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	64 <test>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	65 <param name="rdata_file" value="readBAM__cellcycleM_chrII.RData" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	66 <param name="seq_type" value="paired" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	67 <param name="width" value="147" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	68 <param name="minoverlap" value="80" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	69 <param name="dyad_length" value="50" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	70 <param name="thresholdPercentage" value="35" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	71 <param name="hthres" value="0.4" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	72 <param name="wthres" value="0.6" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	73 <param name="pcKeepComp" value="0.02" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	74 <output name="output_gff_file" file="NR__cellcycleM_chrII.gff" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	75 </test>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	76 </tests>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	77 <help>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	78 .. image:: ${static_path}/images/NucleosomeDynamicsLogo.png
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	79 :height: 80
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	80 :width: 200
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	81
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	82 -----
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	83
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	84 Nucleosome Dynamics is a set of tools that take MNase-seq and ATAC-seq aligned reads and performs a serie of nucleosome-related analyses on them.
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	85
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	86 .. class:: infomark
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	87
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	88 Visit the documentation of the original application for learning more about the accepted values and formats. http://mmb.irbbarcelona.org/NucleosomeDynamics/help/usage/nucleosome-dynamics
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	89 </help>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	90 <citations>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	91 <citation type="bibtex">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	92 @misc{github,
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	93 author = {Buitrago D},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	94 year = {2019},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	95 title = {Nucleosome Dynamics suite: containerized installation},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	96 publisher = {Github},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	97 journal = {GitHub repository},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	98 url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	99 }</citation>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	100 </citations>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	101 </tool>

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e88c806ddf3e Uploaded