Mercurial > repos > spanish_national_institue_of_bioinformatics > nucleosome_dynamics

comparison NFR_stats.xml @ 2:e88c806ddf3e draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author spanish_national_institue_of_bioinformatics
date Fri, 12 Apr 2019 05:28:43 -0400
parents
children
comparison
equal deleted inserted replaced
1:707216744193 2:e88c806ddf3e
1 <tool id="NFR_stats" name="Nucleosome Free Regions Statistics" version="0.1">
2 <description>: gather gene and genome-wide statistics on Nucleosome Free Regions</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 /data:/data -v /tmp:/tmp -u `id -u`:`id -g` mmbirb/nucleosome-dynamics NFR_stats --input $gff_file
9 #if $assembly.source == "buildin":
10 --genome ${assembly.ref_genome_gff_buildin}
11 #else if $assembly.source == "history":
12 --genome ${assembly.ref_genome_gff_history}
13 #end if
14 --out_gw $output_gw_csv_file
15 ]]>
16 </command>
17 <inputs>
18 <param name="gff_file" type="data" format="gff" label="Nucleosome Free Regions (GFF)" help="Nucleosome Free Regions as annotated by NFR tool" />
19 <conditional name="assembly">
20 <param name="source" type="select" label="Select a built-in reference genome or use one from your history" help="Taking from each assembly their annotated genes.">
21 <option value="buildin" selected="True">Use a built-in genome</option>
22 <option value="history">Use a genome from the history</option>
23 </param>
24 <when value="buildin">
25 <param name="ref_genome_gff_buildin" type="select" label="Select reference genome (Genes)" help="Select gene annotations for your reference genome. If your genome of interest is not listed, contact the Galaxy team.">
26 <options from_file="nucldyn_publicdata.loc">
27 <column name="name" index="2"/>
28 <column name="value" index="4"/>
29 </options>
30 </param>
31 </when>
32 <when value="history">
33 <param name="ref_genome_gff_history" type="data" format="gff" label="Reference genome (Genes)" help="Upload gene annotations for your reference genome. Check below the documentation for learning about the file format."/>
34 </when>
35 </conditional>
36 </inputs>
37 <outputs>
38 <data format="csv" name="output_gw_csv_file" label="NFR__stats__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gw.csv" />
39 </outputs>
40 <tests>
41 <test>
42 <param name="gff_file" value="NFR__cellcycleM_chrII.gff" />
43 <param name="ref_genome_gff_buildin" value="/data/nucldyn_publicdata/refGenomes/R64-1-1/genes.gff" />
44 <output name="output_gw_csv_file" file="NFR__stats__cellcycleM_chrII.gw.csv" />
45 </test>
46 </tests>
47 <help>
48 .. image:: ${static_path}/images/NucleosomeDynamicsLogo.png
49 :height: 80
50 :width: 200
51
52 -----
53
54 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.
55
56 .. class:: infomark
57
58 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
59
60 </help>
61 <citations>
62 <citation type="bibtex">
63 @misc{github,
64 author = {Buitrago D},
65 year = {2019},
66 title = {Nucleosome Dynamics suite: containerized installation},
67 publisher = {GitHub},
68 journal = {GitHub repository},
69 url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics},
70 }</citation>
71 </citations>
72 </tool>