diff txstart.xml @ 2:e88c806ddf3e draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/txstart.xml	Fri Apr 12 05:28:43 2019 -0400
@@ -0,0 +1,75 @@
+<tool id="txstart" name="TSS classification" version="0.1">
+  <description>: classify nucleosomes at Transcription Start Sites (TSS)</description>    
+  <requirements>
+  <requirement type="binary">docker</requirement>
+  </requirements>
+  <command>
+	<![CDATA[
+	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 
+		#if $assembly.source == "buildin":
+                	--genome ${assembly.ref_genome_gff_buildin}
+        	#else if $assembly.source == "history":
+                	--genome ${assembly.ref_genome_gff_history}
+        	#end if
+		--output $output_gff_file --window $window --open_thres $open_thres 
+	]]>
+  </command>
+  <inputs>
+    <param name="gff_file" type="data" format="gff" label="Nucleosome calls (GFF)" help="Nucleosome calls in GFF format as obtained from nucleR."/>
+    <conditional name="assembly">
+            <param name="source" type="select" label="Select a built-in reference genome or use one from your history" help="Taking from each assembly their annotated genes.">
+                <option value="buildin" selected="True">Use a built-in genome</option>
+                <option value="history">Use a genome from the history</option>
+            </param>
+            <when value="buildin">
+                <param name="ref_genome_gff_buildin" type="select" label="Select reference genome (Genes)" help="Select gene annotations for your reference genome. If your genome of interest is not listed, contact the Galaxy team.">
+                    <options from_file="nucldyn_publicdata.loc">
+                        <column name="name" index="2"/>
+                        <column name="value" index="4"/>
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="ref_genome_gff_history" type="data" format="gff" label="Reference genome (Genes)" help="Upload gene annotations for your reference genome. Check below the documentation for learning about the file format."/>
+            </when>
+    </conditional>    
+    <param name="window" size="4" type="integer" value="300" label="Window" help="Number of nucleotides on each side of the TSS where -1 and +1 nucleosome are search for." />  
+    <param name="open_thres" size="4" type="integer" value="215" label="Open threshold" help="Distance between nucleosomes -1 and +1 to discriminate between 'open' and 'close' classes." />  
+</inputs>
+  <outputs>
+    <data format="gff" name="output_gff_file" label="TSS__${os.path.splitext(($gff_file.name.split('__'))[1])[0]}.gff" />
+  </outputs>
+<tests>
+	<test>
+		<param name="gff_file" value="NR__cellcycleM_chrII.gff" />
+		<param name="ref_genome_gff_buildin" value="/data/nucldyn_publicdata/refGenomes/R64-1-1/genes.gff" />
+		<param name="window" value="300" />
+		<param name="open_thres" value="215" />
+		<output name="output_gff_file" file="TSS__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>