nucleosome_dynamics: stiffness.xml annotate

annotate stiffness.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="stiffness" name="Stiffness" version="0.1">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	2 <description>: analyze stiffness of nucleosome positioning</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 stiffness --calls $gff_file --reads $rdata_file --output $output_gff_file --range $range
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	9 ]]>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	10 </command>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	11 <inputs>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	12 <param name="gff_file" type="data" format="gff" label="Nucleosome calls (GFF)" help="Nucleosome calls in GFF format as obtained from nucleR."/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	13 <param name="rdata_file" type="data" format="rdata" label="Input MNase-seq/ATAC-seq reads (RData)" help="Input BAM file in RData format as generated by readBAM"/>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	14 <param name="range" size="4" type="text" value="All" label="Genomic Range" help="Genomic region to be analyzed: whole genome ('all'), entire chromosome (chromosome name i.e. 'chrX'), or region of a chromosome ('chromosomeName:start-end)." />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	15 </inputs>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	16 <outputs>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	17 <data format="gff" name="output_gff_file" label="STF__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gff" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	18 </outputs>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	19 <tests>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	20 <test>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	21 <param name="gff_file" value="NR__cellcycleM_chrII.gff" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	22 <param name="rdata_file" value="readBAM__cellcycleM_chrII.RData" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	23 <param name="range" value="All" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	24 <output name="output_gff_file" file="STF__cellcycleM_chrII.gff" />
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	25 </test>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	26 </tests>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	27 <help>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	28 .. image:: ${static_path}/images/NucleosomeDynamicsLogo.png
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	29 :height: 80
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	30 :width: 200
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	31
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	32 -----
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	33
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	34 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	35
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	36 .. class:: infomark
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	37
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	38 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	39 </help>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	40 <citations>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	41 <citation type="bibtex">
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	42 @misc{github,
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	43 author = {Buitrago D},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	44 year = {2019},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	45 title = {Nucleosome Dynamics suite: containerized installation},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	46 publisher = {GitHub},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	47 journal = {GitHub repository},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	48 url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics},
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	49 }</citation>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	50 </citations>
e88c806ddf3e Uploaded spanish_national_institue_of_bioinformatics parents: diff changeset	51 </tool>

Mercurial > repos > spanish_national_institue_of_bioinformatics > nucleosome_dynamics

annotate stiffness.xml @ 2:e88c806ddf3e draft default tip