Mercurial > repos > spanish_national_institue_of_bioinformatics > nucleosome_dynamics
comparison periodicity.xml @ 2:e88c806ddf3e draft default tip
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author | spanish_national_institue_of_bioinformatics |
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date | Fri, 12 Apr 2019 05:28:43 -0400 |
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1:707216744193 | 2:e88c806ddf3e |
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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> |