Mercurial > repos > bgruening > hicexplorer_chicviewpointbackgroundmodel

diff chicViewpointBackgroundModel.xml @ 3:7fe1a401d833 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
author iuc
date Tue, 24 Mar 2020 14:22:19 -0400
parents b9cdce1e57a1
children 628259b7ffb4
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line diff
--- a/chicViewpointBackgroundModel.xml	Wed Mar 11 17:18:30 2020 -0400
+++ b/chicViewpointBackgroundModel.xml	Tue Mar 24 14:22:19 2020 -0400
@@ -18,6 +18,7 @@
             --averageContactBin $averageContactBin
             --fixateRange $fixateRange
             --referencePoints '$referencePoints'
+            $truncateZeros
             --threads @THREADS@
             --outFileName background.txt
     ]]></command>
@@ -29,17 +30,22 @@
                         help="Bed file contains all reference points which should be used to build the background model." />
         <param argument="--averageContactBin" type="integer" value="5"  label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.'/>
         <param argument="--fixateRange" type="integer" value="500000"  label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.'/>
-
+        <param name='truncateZeros' type='boolean' truevalue='--truncateZeros'  falsevalue="" checked="false" label="Truncate zeros"
+                    help="Set this parameter if you want truncate zeros to fight over dispersion."/>
     </inputs>
     <outputs>
         <data name="background" from_work_dir="background.txt" format="tabular" label="${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="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.txt" ftype="tabular" compare="sim_size" delta='40000'/>
+        </test>
+        <test>
+            <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/>
+            <param name="truncateZeros" value="True"/>
+            <param name="referencePoints" value="cHi-C/referencePoints.bed"/>
             <output name="background" file="cHi-C/background.txt" ftype="tabular" compare="sim_size" delta='40000'/>
         </test>
     </tests>