Mercurial > repos > spanish_national_institue_of_bioinformatics > nucleosome_dynamics

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author spanish_national_institue_of_bioinformatics
date Fri, 12 Apr 2019 05:28:43 -0400
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1 <tool id="NFR" name="Nucleosome Free Regions" version="0.1">
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2 <description>: determine Nucleosome Free Regions from nucleR nucleosome calls</description>
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3 <requirements>
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4 <requirement type="binary">docker</requirement>
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5 </requirements>
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6 <command>
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7 <![CDATA[
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8 docker run -v $__root_dir__/database/files:$__root_dir__/database/files -v /tmp:/tmp -u `id -u`:`id -g` mmbirb/nucleosome-dynamics NFR --input $gff_file --output $output_gff_file --minwidth $minwidth --threshold $threshold
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9 ]]>
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10 </command>
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11 <inputs>
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12 <param name="gff_file" type="data" format="gff" label="Nucleosome Calls (GFF)" help="Nucleosome calls in GFF format as obtained from nucleR."/>
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13 <param name="minwidth" size="4" type="integer" value="110" label="Minimum Width" help="Minimum width for a linker fragment to be considered a nucleosome-free region." />
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14 <param name="threshold" size="4" type="integer" value="140" label="Maximum Width" help="Maximum width for a linker fragment to be considered a nucleosome-free region." />
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15 </inputs>
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16 <outputs>
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17 <data format="gff" name="output_gff_file" label="NFR__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gff" />
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name="gff_file" value="NR__cellcycleM_chrII.gff"/>
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22 <param name="minwidth" value="110" />
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23 <param name="threshold" value="400" />
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24 <output name="output_gff_file" file="NFR__cellcycleM_chrII.gff" />
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25 </test>
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26 </tests>
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27 <help>
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28 .. image:: ${static_path}/images/NucleosomeDynamicsLogo.png
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29 :height: 80
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30 :width: 200
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31
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32 -----
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33
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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.
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35
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36 .. class:: infomark
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37
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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
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39 </help>
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40 <citations>
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41 <citation type="bibtex">
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42 @misc{github,
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43 author = {Buitrago D},
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44 year = {2019},
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45 title = {Nucleosome Dynamics suite: containerized installation},
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46 publisher = {GitHub},
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47 journal = {GitHub repository},
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48 url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics},
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49 }</citation>
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50 </citations>
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51 </tool>