nucleosome_dynamics: periodicity.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="periodicity" name="Periodicity" version="0.1">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	2 <description>: analyse nucleosome position phasing and periodicity within genes</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 ln -f -s $bwOutput_file $bwOutput_file\.bw;
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	9 docker run -v $__root_dir__/database/files:$__root_dir__/database/files -v /data:/data -v /tmp:/tmp -u `id -u`:`id -g` mmbirb/nucleosome-dynamics periodicity --calls $gff_file --reads $rdata_file
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	10 #if $assembly.source == "buildin":
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	11 --chrom_sizes ${assembly.ref_chrom_sizes_buildin} --genes ${assembly.ref_genome_gff_buildin}
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	12 #else if $assembly.source == "history":
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	13 --chrom_sizes ${assembly.ref_chrom_sizes} --genes ${assembly.ref_genome_gff_history}
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	14 #end if
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	15 --gffOutput $output_gff_file --type $seq_type --bwOutput $bwOutput_file\.bw --periodicity $periodicity;
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	16 rm $bwOutput_file\.bw
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	17 ]]>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	18 </command>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	19 <inputs>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	20 <param name="gff_file" type="data" format="gff" label="Nucleosome Calls (GFF)" help="Nucleosome calls in GFF format as obtained from nucleR."/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	21 <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	22 <param name="seq_type" type="select" label="Type of sequence reads">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	23 <option value="paired">Paired</option>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	24 <option value="single">Single</option>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	25 </param>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	26 <conditional name="assembly">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	27 <param name="source" type="select" label="Select a built-in reference genome or use one from your history" help="Taking from each assembly their chromosome sizes and their annotated genes.">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	28 <option value="buildin" selected="True">Use a built-in genome</option>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	29 <option value="history">Use a genome from the history</option>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	30 </param>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	31 <when value="buildin">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	32 <param name="ref_chrom_sizes_buildin" type="select" label="Select reference genome (Chrom sizes)" help="Select chromosome size for your reference genome. If your genome of interest is not listed, contact the Galaxy team.">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	33 <options from_file="nucldyn_publicdata.loc">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	34 <column name="name" index="2"/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	35 <column name="value" index="3"/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	36 </options>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	37 </param>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	38 <param name="ref_genome_gff_buildin" type="select" label="Select reference genome (Genes)" help="Select gene annotations for your reference genome. If your genome of interest is not listed, contact the Galaxy team.">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	39 <options from_file="nucldyn_publicdata.loc">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	40 <column name="name" index="2"/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	41 <column name="value" index="4"/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	42 </options>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	43 </param>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	44 </when>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	45 <when value="history">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	46 <param name="ref_chrom_sizes" type="data" format="txt" label="Reference genome (Chrom sizes)" help="Upload chromosome size for your reference genome.Check below the documentation for learning about the file format."/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	47 <param name="ref_genome_gff_history" type="data" format="txt" label="Reference genome (Genes)" help=" Upload gene annotations for your reference genome. Check below the documentation for learning about the file format." />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	48 </when>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	49 </conditional>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	50 <param name="periodicity" size="4" type="integer" value="165" label="Period" help="Average distance between two consecutive nucleosomes (repeat length)." />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	51 </inputs>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	52 <outputs>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	53 <data format="gff" name="output_gff_file" label="P__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gff" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	54 <data format="bigwig" name="bwOutput_file" label="P__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.bw" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	55 </outputs>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	56 <tests>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	57 <test>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	58 <param name="gff_file" value="NR__cellcycleM_chrII.gff" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	59 <param name="rdata_file" value="readBAM__cellcycleM_chrII.RData" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	60 <param name="seq_type" value="paired" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	61 <param name="ref_chrom_sizes_buildin" value="/data/nucldyn_publicdata/refGenomes/R64-1-1/R64-1-1.fa.chrom.sizes" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	62 <param name="ref_genome_gff_buildin" value="/data/nucldyn_publicdata/refGenomes/R64-1-1/genes.gff" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	63 <param name="periodicity" value="165" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	64 <output name="output_gff_file" value="P__cellcycleM_chrII.gff" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	65 <output name="bwOutput_file" value="P__cellcycleM_chrII.bw"/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	66 </test>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	67 </tests>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	68 <help>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	69 .. image:: ${static_path}/images/NucleosomeDynamicsLogo.png
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	70 :height: 80
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	71 :width: 200
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	72
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	73 -----
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	74
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	75 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	76
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	77 .. class:: infomark
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	78
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	79 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	80 </help>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	81 <citations>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	82 <citation type="bibtex">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	83 @misc{github,
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	84 author = {Buitrago D},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	85 year = {2019},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	86 title = {Nucleosome Dynamics suite: containerized installation},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	87 publisher = {GitHub},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	88 journal = {GitHub repository},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	89 url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	90 }</citation>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	91 </citations>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	92 </tool>

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e88c806ddf3e Uploaded