Mercurial > repos > spanish_national_institue_of_bioinformatics > nucleosome_dynamics
comparison stiffness.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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| 1:707216744193 | 2:e88c806ddf3e |
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| 1 <tool id="stiffness" name="Stiffness" version="0.1"> | |
| 2 <description>: analyze stiffness of nucleosome positioning</description> | |
| 3 <requirements> | |
| 4 <requirement type="binary">docker</requirement> | |
| 5 </requirements> | |
| 6 <command> | |
| 7 <![CDATA[ | |
| 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 $range | |
| 9 ]]> | |
| 10 </command> | |
| 11 <inputs> | |
| 12 <param name="gff_file" type="data" format="gff" label="Nucleosome calls (GFF)" help="Nucleosome calls in GFF format as obtained from nucleR."/> | |
| 13 <param name="rdata_file" type="data" format="rdata" label="Input MNase-seq/ATAC-seq reads (RData)" help="Input BAM file in RData format as generated by readBAM"/> | |
| 14 <param name="range" size="4" type="text" value="All" label="Genomic Range" help="Genomic region to be analyzed: whole genome ('all'), entire chromosome (chromosome name i.e. 'chrX'), or region of a chromosome ('chromosomeName:start-end)." /> | |
| 15 </inputs> | |
| 16 <outputs> | |
| 17 <data format="gff" name="output_gff_file" label="STF__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gff" /> | |
| 18 </outputs> | |
| 19 <tests> | |
| 20 <test> | |
| 21 <param name="gff_file" value="NR__cellcycleM_chrII.gff" /> | |
| 22 <param name="rdata_file" value="readBAM__cellcycleM_chrII.RData" /> | |
| 23 <param name="range" value="All" /> | |
| 24 <output name="output_gff_file" file="STF__cellcycleM_chrII.gff" /> | |
| 25 </test> | |
| 26 </tests> | |
| 27 <help> | |
| 28 .. image:: ${static_path}/images/NucleosomeDynamicsLogo.png | |
| 29 :height: 80 | |
| 30 :width: 200 | |
| 31 | |
| 32 ----- | |
| 33 | |
| 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. | |
| 35 | |
| 36 .. class:: infomark | |
| 37 | |
| 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 | |
| 39 </help> | |
| 40 <citations> | |
| 41 <citation type="bibtex"> | |
| 42 @misc{github, | |
| 43 author = {Buitrago D}, | |
| 44 year = {2019}, | |
| 45 title = {Nucleosome Dynamics suite: containerized installation}, | |
| 46 publisher = {GitHub}, | |
| 47 journal = {GitHub repository}, | |
| 48 url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics}, | |
| 49 }</citation> | |
| 50 </citations> | |
| 51 </tool> |