Mercurial > repos > bgruening > hicexplorer_chicsignificantinteractions

diff chicSignificantInteractions.xml @ 3:7668fac6cc3a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"
author iuc
date Tue, 24 Mar 2020 13:42:40 -0400
parents 3df84bb4486c
children 38fa8a72ece6
line wrap: on
line diff
--- a/chicSignificantInteractions.xml	Wed Mar 11 16:54:59 2020 -0400
+++ b/chicSignificantInteractions.xml	Tue Mar 24 13:42:40 2020 -0400
@@ -49,8 +49,7 @@
             --range $rangeUpstream $rangeDownstream
             --targetFolder targetFolder
             --outputFolder significantFilesFolder
-
-            --xFoldMaxValueNB $xFoldMaxValueNB
+            $truncateZeroPvalues
             --fixateRange $fixateRange
             -suffix significant_interactions.txt
             --threads @THREADS@
@@ -95,7 +94,8 @@
         <param name="rangeUpstream" type="integer" value="500000"  label="Upstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' />
         <param name="rangeDownstream" type="integer" value="500000"  label="Downstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' />
         <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 argument="--xFoldMaxValueNB" type="integer" value="10"  label="x-fold for NB distributions" help='x-fold factor to increase the number of precomputed p-values per relative genomic distance. If set to 1, the maximal distance is used.'/>
+        <param name='truncateZeroPvalues' type='boolean' truevalue='--truncateZeroPvalues'  falsevalue="" checked="false" label="Truncate zeros by setting them to one."
+                    help="Sets all p-values which are equal to zero to one. This has the effect that the associated positions are not part of the significance decision."/>
     </inputs>
     <outputs>
         <collection name="significantFilesCollection" type="list" label="Significant files">
@@ -131,13 +131,13 @@
             <param name="rangeDownstream" value="200000"/>
 
             <output_collection name="significantFilesCollection" type="list" count="6">
-                <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt" ftype="interval" lines_diff="4"/>
-                <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt" ftype="interval" lines_diff="4"/>
-                <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt" ftype="interval" lines_diff="4"/>
+                <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" ftype="interval" lines_diff="4"/>
+                <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" ftype="interval" lines_diff="4"/>
+                <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" ftype="interval" lines_diff="4"/>
 
-                <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt" ftype="interval" lines_diff="4"/>
-                <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt" ftype="interval" lines_diff="4"/>
-                <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt" ftype="interval" lines_diff="4"/>
+                <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" ftype="interval" lines_diff="4"/>
+                <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" ftype="interval" lines_diff="4"/>
+                <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" ftype="interval" lines_diff="4"/>
             </output_collection>
 
             <output_collection name="targetFilesCollection" type="list" count="3">