diff chicViewpointBackgroundModel.xml @ 0:bd11c6a972ef draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chicViewpointBackgroundModel.xml	Mon Dec 16 15:32:01 2019 -0500
@@ -0,0 +1,62 @@
+<tool id="hicexplorer_chicviewpointbackgroundmodel" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>validate detected loops with protein peaks.</description>
+    <macros>
+        <token name="@BINARY@">chicViewpointBackgroundModel</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+   
+        #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
+            ln -s '$m' '${counter}_matrix.$m.ext' &&
+        #end for
+        #set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
+       
+        @BINARY@
+
+            --matrices $m
+            --averageContactBin $averageContactBin
+            --fixateRange $fixateRange
+            --referencePoints '$referencePoints'
+            --threads @THREADS@
+            --outFileName background.txt
+    ]]></command>
+    <inputs>
+        <expand macro="matrix_h5_cooler_multiple_macro" />
+       
+        <param argument="--referencePoints" type="data" format='interval'
+                        label="Reference points"
+                        help="Bed file contains all reference points which should be used to build the background model." />
+        <param argument="--averageContactBin" type="integer" value="5"  label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.'/>    
+        <param argument="--fixateRange" type="integer" value="500000"  label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.'/>    
+   
+    </inputs>
+    <outputs>
+        <data name="background" from_work_dir="background.txt" format="tabular" label="${tool.name} on [${on_string}]: Background model"/>
+    </outputs>
+    <tests>
+        <test>
+           <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/>
+            
+            <param name="referencePoints" value="cHi-C/referencePoints.bed"/>
+           
+            <output name="background" file="cHi-C/background.bed" ftype="tabular" compare="sim_size" delta='40000'/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Compute a background model for cHi-C data analysis
+==================================================
+
+chicViewpointBackgroundModel computes for all given samples with all reference points a background model. For all relative distances to a reference point
+a negative binomial distribution is fitted. Moreover, for each relative distance to a reference point the average value for this location is computed. Both
+background models are used, the first one for p-value and significance computation, the second one to filter out interactions with a less x-fold over mean.
+
+The background distributions are fixed at `--fixateRange` i.e. all distances lower / higher than this value use the fixed background distribution.
+
+For more information about HiCExplorer please consider our documentation on readthedocs.io_
+
+.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
+]]></help>
+    <expand macro="citations" />
+</tool>