Mercurial > repos > spanish_national_institue_of_bioinformatics > nucleosome_dynamics

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