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comparison readBAM.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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1:707216744193 2:e88c806ddf3e
1 <tool id="readBAM" name="readBAM" version="0.1">
2 <description>: convert aligned BAM files to RData format for NucleosomeDynamics</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 /tmp:/tmp -u `id -u`:`id -g` mmbirb/nucleosome-dynamics readBAM --input $bam_file --output $rdata_file --type $seq_type
9 ]]>
10 </command>
11 <inputs>
12 <param name="bam_file" type="data" format="bam" label="MNase-seq / ATAC-seq BAM file" help="Upload your MNase-seq or ATAC-seq reads file in BAM format. Access sample data at 'Shared Data -> Data libraries" />
13 <param name="seq_type" type="select" label="Type of sequence reads">
14 <option value="paired">Paired</option>
15 <option value="single">Single</option>
16 </param>
17 </inputs>
18 <outputs>
19 <data format="rdata" name="rdata_file" label="readBAM__${os.path.splitext(os.path.basename($bam_file.name))[0]}.rdata" />
20 </outputs>
21 <tests>
22 <test>
23 <param name="bam_file" value="cellcycleM_chrII.bam"/>
24 <param name="seq_type" value="paired" />
25 <output name="rdata_file" file="readBAM__cellcycleM_chrII.RData"/>
26 </test>
27 </tests>
28 <help>
29 .. image:: ${static_path}/images/NucleosomeDynamicsLogo.png
30 :height: 80
31 :width: 200
32
33 -----
34
35 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.
36
37 .. class:: infomark
38
39 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
40
41 </help>
42 <citations>
43 <citation type="bibtex">
44 @misc{github,
45 author = {Buitrago D},
46 year = {2019},
47 title = {Nucleosome Dynamics suite: containerized installation},
48 publisher = {GitHub},
49 journal = {GitHub repository},
50 url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics},
51 }</citation>
52 </citations>
53 </tool>