Mercurial > repos > spanish_national_institue_of_bioinformatics > nucleosome_dynamics

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