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comparison periodicity.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 <tool id="periodicity" name="Periodicity" version="0.1">
2 <description>: analyse nucleosome position phasing and periodicity within genes</description>
3 <requirements>
4 <requirement type="binary">docker</requirement>
5 </requirements>
6 <command>
7 <![CDATA[
8 ln -f -s $bwOutput_file $bwOutput_file\.bw;
9 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 periodicity --calls $gff_file --reads $rdata_file
10 #if $assembly.source == "buildin":
11 --chrom_sizes ${assembly.ref_chrom_sizes_buildin} --genes ${assembly.ref_genome_gff_buildin}
12 #else if $assembly.source == "history":
13 --chrom_sizes ${assembly.ref_chrom_sizes} --genes ${assembly.ref_genome_gff_history}
14 #end if
15 --gffOutput $output_gff_file --type $seq_type --bwOutput $bwOutput_file\.bw --periodicity $periodicity;
16 rm $bwOutput_file\.bw
17 ]]>
18 </command>
19 <inputs>
20 <param name="gff_file" type="data" format="gff" label="Nucleosome Calls (GFF)" help="Nucleosome calls in GFF format as obtained from nucleR."/>
21 <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"/>
22 <param name="seq_type" type="select" label="Type of sequence reads">
23 <option value="paired">Paired</option>
24 <option value="single">Single</option>
25 </param>
26 <conditional name="assembly">
27 <param name="source" type="select" label="Select a built-in reference genome or use one from your history" help="Taking from each assembly their chromosome sizes and their annotated genes.">
28 <option value="buildin" selected="True">Use a built-in genome</option>
29 <option value="history">Use a genome from the history</option>
30 </param>
31 <when value="buildin">
32 <param name="ref_chrom_sizes_buildin" type="select" label="Select reference genome (Chrom sizes)" help="Select chromosome size for your reference genome. If your genome of interest is not listed, contact the Galaxy team.">
33 <options from_file="nucldyn_publicdata.loc">
34 <column name="name" index="2"/>
35 <column name="value" index="3"/>
36 </options>
37 </param>
38 <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.">
39 <options from_file="nucldyn_publicdata.loc">
40 <column name="name" index="2"/>
41 <column name="value" index="4"/>
42 </options>
43 </param>
44 </when>
45 <when value="history">
46 <param name="ref_chrom_sizes" type="data" format="txt" label="Reference genome (Chrom sizes)" help="Upload chromosome size for your reference genome.Check below the documentation for learning about the file format."/>
47 <param name="ref_genome_gff_history" type="data" format="txt" label="Reference genome (Genes)" help=" Upload gene annotations for your reference genome. Check below the documentation for learning about the file format." />
48 </when>
49 </conditional>
50 <param name="periodicity" size="4" type="integer" value="165" label="Period" help="Average distance between two consecutive nucleosomes (repeat length)." />
51 </inputs>
52 <outputs>
53 <data format="gff" name="output_gff_file" label="P__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gff" />
54 <data format="bigwig" name="bwOutput_file" label="P__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.bw" />
55 </outputs>
56 <tests>
57 <test>
58 <param name="gff_file" value="NR__cellcycleM_chrII.gff" />
59 <param name="rdata_file" value="readBAM__cellcycleM_chrII.RData" />
60 <param name="seq_type" value="paired" />
61 <param name="ref_chrom_sizes_buildin" value="/data/nucldyn_publicdata/refGenomes/R64-1-1/R64-1-1.fa.chrom.sizes" />
62 <param name="ref_genome_gff_buildin" value="/data/nucldyn_publicdata/refGenomes/R64-1-1/genes.gff" />
63 <param name="periodicity" value="165" />
64 <output name="output_gff_file" value="P__cellcycleM_chrII.gff" />
65 <output name="bwOutput_file" value="P__cellcycleM_chrII.bw"/>
66 </test>
67 </tests>
68 <help>
69 .. image:: ${static_path}/images/NucleosomeDynamicsLogo.png
70 :height: 80
71 :width: 200
72
73 -----
74
75 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.
76
77 .. class:: infomark
78
79 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
80 </help>
81 <citations>
82 <citation type="bibtex">
83 @misc{github,
84 author = {Buitrago D},
85 year = {2019},
86 title = {Nucleosome Dynamics suite: containerized installation},
87 publisher = {GitHub},
88 journal = {GitHub repository},
89 url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics},
90 }</citation>
91 </citations>
92 </tool>