Mercurial > repos > spanish_national_institue_of_bioinformatics > nucleosome_dynamics
diff nucDyn.xml @ 2:e88c806ddf3e draft default tip
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| author | spanish_national_institue_of_bioinformatics |
|---|---|
| date | Fri, 12 Apr 2019 05:28:43 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nucDyn.xml Fri Apr 12 05:28:43 2019 -0400 @@ -0,0 +1,117 @@ +<tool id="nucDyn" name="Nucleosome Dynamics" version="0.1"> + <description>: detection of local changes in the position of nucleosomes, observed between two reference nucleosome maps </description> + <requirements> + <requirement type="binary">docker</requirement> + </requirements> + <command> +<![CDATA[ + ln -f -s $output_bw_file $output_bw_file\.bw; + 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 + #if $assembly.source == "buildin": + --genome ${assembly.ref_chrom_sizes_buildin} + #else if $assembly.source == "history": + --genome ${assembly.ref_chrom_sizes} + #end if + + #if $maxdiff + --maxDiff $maxdiff + #end if + #if $maxlen + --maxLen $maxlen + #end if + #if $minreads + --shift_min_nreads $minreads + #end if + #if $threshold + --shift_threshold $threshold + #end if + #if $minread + --indel_min_nreads $minread + #end if + #if $indthreshold + --indel_threshold $indthreshold + #end if + + --range $range --equal_size $equal --readSize $readsize ; + rm $output_bw_file\.bw +]]> + </command> + <inputs> + <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."/> + <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"/> + <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. "/> + <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."/> + <conditional name="assembly"> + <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."> + <option value="buildin" selected="True">Use a built-in genome</option> + <option value="history">Use a genome from the history</option> + </param> + <when value="buildin"> + <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"> + <options from_file="nucldyn_publicdata.loc"> + <column name="name" index="2"/> + <column name="value" index="3"/> + </options> + </param> + </when> + <when value="history"> + <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."/> + </when> + </conditional> + <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."/> + <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."/> + <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."/> + <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."/> + <param name="threshold" type="float" value="0.1" label="Shifts threshold" optional="True" help="Minimum score for a 'SHIFT +' or a 'SHIFT -' hotspot."/> + <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" /> + <param name="indthreshold" type="float" value="0.05" label="Indels threshold" optional="True" help="Minimum score for an 'INCLUSION' or a 'DELETION' hotspot." /> + <param name="equal" type="boolean" checked="false" label="Use Equal Size" optional="True" help="Set all fragments to the same size."/> + <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`." /> + </inputs> + <outputs> + <data format="gff" name="output_gff_file" label="ND__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}_${os.path.splitext(($gff_file2.name.split('__'))[1])[0]}.gff"/> + <data format="bigwig" name="output_bw_file" label="ND__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}_${os.path.splitext(($gff_file2.name.split('__'))[1])[0]}.bw"/> + </outputs> + <tests> + <test> + <param name="rdata_file" value="readBAM__cellcycleG2_chrII.RData" /> + <param name="rdata_file2" value="readBAM__cellcycleM_chrII.RData" /> + <param name="gff_file" value="NR__cellcycleG2_chrII.gff" /> + <param name="gff_file2" value="NR__cellcycleM_chrII.gff" /> + <param name="ref_chrom_sizes_buildin" value="/data/nucldyn_publicdata/refGenomes/R64-1-1/R64-1-1.fa.chrom.sizes" /> + <param name="range" value="All" /> + <param name="maxdiff" value="70" /> + <param name="maxlen" value="140" /> + <param name="minreads" value="3" /> + <param name="threshold" value="0.1" /> + <param name="minread" value="3" /> + <param name="indthreshold" value="0.05" /> + <output name="output_gff_file" file="ND__cellcycleG2_chrII_cellcycleM_chrII.gff" /> + <output name="output_bw_file" file="ND__cellcycleG2_chrII_cellcycleM_chrII.bw" /> + </test> + </tests> + <help> + .. image:: ${static_path}/images/NucleosomeDynamicsLogo.png + :height: 80 + :width: 200 + +----- + +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. + +.. class:: infomark + +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 + </help> + <citations> + <citation type="bibtex"> +@misc{github, + author = {Buitrago D}, + year = {2019}, + title = {Nucleosome Dynamics suite: containerized installation}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics}, +}</citation> + </citations> +</tool>