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comparison txstart.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="txstart" name="TSS classification" version="0.1">
2 <description>: classify nucleosomes at Transcription Start Sites (TSS)</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 txstart --calls $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 --output $output_gff_file --window $window --open_thres $open_thres
15 ]]>
16 </command>
17 <inputs>
18 <param name="gff_file" type="data" format="gff" label="Nucleosome calls (GFF)" help="Nucleosome calls in GFF format as obtained from nucleR."/>
19 <conditional name="assembly">
20 <param name="source" type="select" label="Select a built-in reference genome or use one from your history" help="Taking from each assembly their annotated genes.">
21 <option value="buildin" selected="True">Use a built-in genome</option>
22 <option value="history">Use a genome from the history</option>
23 </param>
24 <when value="buildin">
25 <param name="ref_genome_gff_buildin" type="select" label="Select reference genome (Genes)" help="Select gene annotations for your reference genome. If your genome of interest is not listed, contact the Galaxy team.">
26 <options from_file="nucldyn_publicdata.loc">
27 <column name="name" index="2"/>
28 <column name="value" index="4"/>
29 </options>
30 </param>
31 </when>
32 <when value="history">
33 <param name="ref_genome_gff_history" type="data" format="gff" label="Reference genome (Genes)" help="Upload gene annotations for your reference genome. Check below the documentation for learning about the file format."/>
34 </when>
35 </conditional>
36 <param name="window" size="4" type="integer" value="300" label="Window" help="Number of nucleotides on each side of the TSS where -1 and +1 nucleosome are search for." />
37 <param name="open_thres" size="4" type="integer" value="215" label="Open threshold" help="Distance between nucleosomes -1 and +1 to discriminate between 'open' and 'close' classes." />
38 </inputs>
39 <outputs>
40 <data format="gff" name="output_gff_file" label="TSS__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gff" />
41 </outputs>
42 <tests>
43 <test>
44 <param name="gff_file" value="NR__cellcycleM_chrII.gff" />
45 <param name="ref_genome_gff_buildin" value="/data/nucldyn_publicdata/refGenomes/R64-1-1/genes.gff" />
46 <param name="window" value="300" />
47 <param name="open_thres" value="215" />
48 <output name="output_gff_file" file="TSS__cellcycleM_chrII.gff" />
49 </test>
50 </tests>
51 <help>
52 .. image:: ${static_path}/images/NucleosomeDynamicsLogo.png
53 :height: 80
54 :width: 200
55
56 -----
57
58 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.
59
60 .. class:: infomark
61
62 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
63 </help>
64 <citations>
65 <citation type="bibtex">
66 @misc{github,
67 author = {Buitrago D},
68 year = {2019},
69 title = {Nucleosome Dynamics suite: containerized installation},
70 publisher = {GitHub},
71 journal = {GitHub repository},
72 url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics},
73 }</citation>
74 </citations>
75 </tool>