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diff stiffness.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/stiffness.xml	Fri Apr 12 05:28:43 2019 -0400
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+<tool id="stiffness" name="Stiffness" version="0.1">
+  <description>: analyze stiffness of nucleosome positioning</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 stiffness --calls $gff_file --reads $rdata_file --output $output_gff_file --range $range
+	]]>
+  </command>
+  <inputs>
+    <param name="gff_file" type="data" format="gff" label="Nucleosome calls (GFF)" help="Nucleosome calls in GFF format as obtained from nucleR."/>
+    <param name="rdata_file" type="data" format="rdata" label="Input MNase-seq/ATAC-seq reads (RData)" help="Input BAM file in RData format as generated by readBAM"/>
+    <param name="range" size="4" type="text" value="All" label="Genomic Range" help="Genomic region to be analyzed: whole genome ('all'), entire chromosome (chromosome name i.e. 'chrX'), or region of a chromosome ('chromosomeName:start-end)." />  
+</inputs>
+  <outputs>
+    <data format="gff" name="output_gff_file" label="STF__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gff" />
+  </outputs>
+  <tests>
+	  <test>
+		  <param name="gff_file" value="NR__cellcycleM_chrII.gff" />
+		  <param name="rdata_file" value="readBAM__cellcycleM_chrII.RData" />
+		  <param name="range" value="All" />
+		  <output name="output_gff_file" file="STF__cellcycleM_chrII.gff" />
+	  </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>