diff chicPlotViewpoint.xml @ 3:dbf82dd7bdb3 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3d3fe0c7636592f01981d491dc8ff44bb55c1750"

--- a/chicPlotViewpoint.xml	Wed Mar 11 17:14:05 2020 -0400
+++ b/chicPlotViewpoint.xml	Tue Mar 24 14:12:09 2020 -0400
@@ -100,7 +100,7 @@
             #end if
             --colorList $colorList
             --threads @THREADS@
-
+            $truncateZeroPvalues
             #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
                 && mv out_plot.$image_file_format plots/out_plot.$image_file_format
             #end if
@@ -148,7 +148,9 @@
         </param>
         <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
         <param name='colorList' type='text' value='g b c m y k' label='Color list' help='Colorlist for the viewpoint lines. For all available colors please check matplotlib documentation: https://matplotlib.org/3.1.0/gallery/color/named_colors.html' optional='true'/>
-
+        <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 disturbing the presenation of small p-values."/>
+  
 
     </inputs>
     <outputs>
@@ -161,7 +163,7 @@
         <test>
             <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt"/>
             <param name="differentialFiles" value="cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt"/>
-            <param name="significantFiles" value="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.txt"/>
+            <param name="significantFiles" value="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt"/>
 
 
             <conditional name="batchmode_conditional">
@@ -172,7 +174,9 @@
                 <param name='computeSampleNumber' value='2'/>
             </conditional>
             <param name="pvalue" value='True'/>
-            <param name="alpha" value='0.5'/>
+            <param name="truncateZeroPvalues" value='True'/>
+
+            <!-- <param name="alpha" value='0.5'/> -->
             <param name='backgroundModelFile' value='cHi-C/background.txt'/>
             <param name='xFold' value='1.5'/>
             <output_collection name="plotsCollection" type="list" count="3">
@@ -194,6 +198,19 @@
 
             </output_collection>
         </test>
+
+        <test>
+            <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt"/>
+
+            <conditional name="batchmode_conditional">
+                <param name="batchmode_selector" value='optionSinglemode'/>
+            </conditional>
+
+            <output_collection name="plotsCollection" type="list" count="1">
+                <element name="out_plot" file="cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png" ftype="png" compare='sim_size' delta='40000'/>
+
+            </output_collection>
+        </test>
     </tests>
     <help><![CDATA[