nucleosome_dynamics: nucDyn.xml annotate

annotate nucDyn.xml @ 2:e88c806ddf3e draft default tip

Uploaded

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="nucDyn" name="Nucleosome Dynamics" version="0.1">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	2 <description>: detection of local changes in the position of nucleosomes, observed between two reference nucleosome maps </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 $output_bw_file $output_bw_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 nucDyn --input1 $rdata_file --input2 $rdata_file2 --calls1 $gff_file --calls2 $gff_file2 --outputGff $output_gff_file --outputBigWig $output_bw_file\.bw
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 --genome ${assembly.ref_chrom_sizes_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 --genome ${assembly.ref_chrom_sizes}
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	14 #end if
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	15
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	16 #if $maxdiff
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	17 --maxDiff $maxdiff
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	18 #end if
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	19 #if $maxlen
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	20 --maxLen $maxlen
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	21 #end if
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	22 #if $minreads
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	23 --shift_min_nreads $minreads
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	24 #end if
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	25 #if $threshold
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	26 --shift_threshold $threshold
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	27 #end if
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	28 #if $minread
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	29 --indel_min_nreads $minread
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	30 #end if
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	31 #if $indthreshold
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	32 --indel_threshold $indthreshold
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	33 #end if
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	34
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	35 --range $range --equal_size $equal --readSize $readsize ;
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	36 rm $output_bw_file\.bw
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	37 ]]>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	38 </command>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	39 <inputs>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	40 <param name="rdata_file" type="data" format="rdata" label="Condition 1: MNase-seq reference reads (Rdata)" help="Input BAM from MNase-seq in RData format for the initial state to be compared."/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	41 <param name="gff_file" type="data" format="gff" label="Condition 1: MNase-seq reference nucleosomes (GFF)" help="Nucleosome calls in GFF format as obtained from nucleR for the initial state to be compared"/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	42 <param name="rdata_file2" type="data" format="rdata" label="Condition 2: MNase-seq final reads (Rdata)" help="Input BAM from MNase-seq in RData format for the final state to be compared. "/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	43 <param name="gff_file2" type="data" format="gff" label="Condition 2: MNase-seq final nucleosomes (GFF)" help="Nucleosome calls in GFF format as obtained from nucleR for the final state to be compared."/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	44 <conditional name="assembly">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	45 <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.">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	46 <option value="buildin" selected="True">Use a built-in genome</option>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	47 <option value="history">Use a genome from the history</option>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	48 </param>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	49 <when value="buildin">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	50 <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	51 <options from_file="nucldyn_publicdata.loc">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	52 <column name="name" index="2"/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	53 <column name="value" index="3"/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	54 </options>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	55 </param>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	56 </when>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	57 <when value="history">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	58 <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	59 </when>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	60 </conditional>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	61 <param name="range" type="text" value="All" label="Range" help="Genomic region to be analyzed: whole genome ('all'), entire chromosome (chromosome name i.e. 'chrX'), or region of a chromosome."/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	62 <param name="maxdiff" type="integer" value="70" label="Maximum Diff" optional="True" help="Maximum distance between the dyads of two reads that allows them to still be considered a shift. If unspecified but readSize is specified, it will be set to the half of readSize. If neither of them is specified, it will be set to 70."/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	63 <param name="maxlen" type="integer" value="140" label="Maximum Lenght" optional="True" help="Used in the preliminar filtering. Reads longer than this number will be filtered out."/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	64 <param name="minreads" type="integer" value="3" label="Shift minimum num. reads" optional="True" help="Minimum number of reads in a 'SHIFT +' or a 'SHIFT -' hotspot."/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	65 <param name="threshold" type="float" value="0.1" label="Shifts threshold" optional="True" help="Minimum score for a 'SHIFT +' or a 'SHIFT -' hotspot."/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	66 <param name="minread" type="integer" value="3" label="Indels minimum num. reads" optional="True" help="Minimum number of reads in an 'INCLUSION +' or a 'DELETION -' hotspot" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	67 <param name="indthreshold" type="float" value="0.05" label="Indels threshold" optional="True" help="Minimum score for an 'INCLUSION' or a 'DELETION' hotspot." />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	68 <param name="equal" type="boolean" checked="false" label="Use Equal Size" optional="True" help="Set all fragments to the same size."/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	69 <param name="readsize" type="integer" value="140" label="Read Size" help="Length to which all reads will be set in case `equalSize` is `TRUE`. It is ignored when `equalSize` is set to `FALSE`." />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	70 </inputs>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	71 <outputs>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	72 <data format="gff" name="output_gff_file" label="ND__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}_${os.path.splitext(($gff_file2.name.split('__'))[1])[0]}.gff"/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	73 <data format="bigwig" name="output_bw_file" label="ND__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}_${os.path.splitext(($gff_file2.name.split('__'))[1])[0]}.bw"/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	74 </outputs>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	75 <tests>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	76 <test>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	77 <param name="rdata_file" value="readBAM__cellcycleG2_chrII.RData" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	78 <param name="rdata_file2" value="readBAM__cellcycleM_chrII.RData" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	79 <param name="gff_file" value="NR__cellcycleG2_chrII.gff" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	80 <param name="gff_file2" value="NR__cellcycleM_chrII.gff" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	81 <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	82 <param name="range" value="All" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	83 <param name="maxdiff" value="70" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	84 <param name="maxlen" value="140" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	85 <param name="minreads" value="3" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	86 <param name="threshold" value="0.1" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	87 <param name="minread" value="3" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	88 <param name="indthreshold" value="0.05" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	89 <output name="output_gff_file" file="ND__cellcycleG2_chrII_cellcycleM_chrII.gff" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	90 <output name="output_bw_file" file="ND__cellcycleG2_chrII_cellcycleM_chrII.bw" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	91 </test>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	92 </tests>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	93 <help>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	94 .. image:: ${static_path}/images/NucleosomeDynamicsLogo.png
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	95 :height: 80
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	96 :width: 200
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	97
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	98 -----
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	99
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	100 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	101
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	102 .. class:: infomark
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	103
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	104 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	105 </help>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	106 <citations>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	107 <citation type="bibtex">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	108 @misc{github,
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	109 author = {Buitrago D},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	110 year = {2019},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	111 title = {Nucleosome Dynamics suite: containerized installation},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	112 publisher = {GitHub},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	113 journal = {GitHub repository},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	114 url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	115 }</citation>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	116 </citations>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	117 </tool>

Mercurial > repos > spanish_national_institue_of_bioinformatics > nucleosome_dynamics

annotate nucDyn.xml @ 2:e88c806ddf3e draft default tip