Mercurial > repos > spanish_national_institue_of_bioinformatics > nucleosome_dynamics

diff 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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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readBAM.xml	Fri Apr 12 05:28:43 2019 -0400
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+<tool id="readBAM" name="readBAM" version="0.1">
+  <description>: convert aligned BAM files to RData format for NucleosomeDynamics</description>
+  <requirements>
+  <requirement type="binary">docker</requirement>
+  </requirements>
+  <command>
+<![CDATA[
+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 $seq_type
+]]>
+  </command>
+  <inputs>
+    <param name="bam_file" type="data" format="bam" label="MNase-seq / ATAC-seq BAM file" help="Upload your MNase-seq or ATAC-seq reads file in BAM format. Access sample data at 'Shared Data -> Data libraries" />
+    <param name="seq_type" type="select" label="Type of sequence reads">
+      <option value="paired">Paired</option>
+      <option value="single">Single</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="rdata" name="rdata_file" label="readBAM__${os.path.splitext(os.path.basename($bam_file.name))[0]}.rdata" />
+  </outputs>
+  <tests>
+      <test>   
+	  <param  name="bam_file" value="cellcycleM_chrII.bam"/>
+          <param  name="seq_type" value="paired" />
+	  <output name="rdata_file" file="readBAM__cellcycleM_chrII.RData"/>
+       </test>
+   </tests>
+   <help>
+ .. image:: ${static_path}/images/NucleosomeDynamicsLogo.png
+    :height: 80
+    :width: 200
+
+-----
+
+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.
+
+.. class:: infomark
+
+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
+
+   </help>
+   <citations>
+        <citation type="bibtex">
+@misc{github,
+  author = {Buitrago D},
+  year = {2019},
+  title = {Nucleosome Dynamics suite: containerized installation},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/nucleosome-dynamics/nucleosome_dynamics},
+}</citation>
+ </citations>
+</tool>