comparison NFR.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
1 <tool id="NFR" name="Nucleosome Free Regions" version="0.1">
2 <description>: determine Nucleosome Free Regions from nucleR nucleosome calls</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 NFR --input $gff_file --output $output_gff_file --minwidth $minwidth --threshold $threshold
9 ]]>
10 </command>
11 <inputs>
12 <param name="gff_file" type="data" format="gff" label="Nucleosome Calls (GFF)" help="Nucleosome calls in GFF format as obtained from nucleR."/>
13 <param name="minwidth" size="4" type="integer" value="110" label="Minimum Width" help="Minimum width for a linker fragment to be considered a nucleosome-free region." />
14 <param name="threshold" size="4" type="integer" value="140" label="Maximum Width" help="Maximum width for a linker fragment to be considered a nucleosome-free region." />
15 </inputs>
16 <outputs>
17 <data format="gff" name="output_gff_file" label="NFR__${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="minwidth" value="110" />
23 <param name="threshold" value="400" />
24 <output name="output_gff_file" file="NFR__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>