diff hicPlotMatrix.xml @ 19:e8ea78b11ce6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"

--- a/hicPlotMatrix.xml	Thu Feb 06 00:18:11 2020 +0000
+++ b/hicPlotMatrix.xml	Tue Mar 10 18:23:45 2020 +0000
@@ -16,7 +16,7 @@
         ln -s $matrix_h5_cooler matrix.$matrix_h5_cooler.ext &&
         @BINARY@
 
-            
+
             --matrix 'matrix.$matrix_h5_cooler.ext'
 
             #if $title and $title is not None:
@@ -59,18 +59,37 @@
             #if $vMax:
                 --vMax $vMax
             #end if
-            
+
             #if str($pca_conditional.pca_type) == 'bigwig':
-                --vMinBigwig $pca_conditional.vMinBigwig
-                --vMaxBigwig $pca_conditional.vMaxBigwig
+                #if $pca_conditional.vMinBigwig:
+                    --vMinBigwig $pca_conditional.vMinBigwig
+                #end if
+                #if $pca_conditional.vMaxBigwig:
+                    --vMaxBigwig $pca_conditional.vMaxBigwig
+                #end if
                 $pca_conditional.flipBigwigSign
-                --scaleFactorBigwig $pca_conditional.scaleFactorBigwig
+
+                #if $pca_conditional.scaleFactorBigwig:
+                    --scaleFactorBigwig $pca_conditional.scaleFactorBigwig
+                #end if
                 $pca_conditional.bigwigAdditionalVerticalAxis
-            #end if 
+            #end if
             $pca
             #if $dpi:
                 --dpi $dpi
-            #end if 
+            #end if
+
+            #if $fontSize:
+                --fontSize $fontSize
+            #end if
+
+            #if $rotationX:
+                --rotationX $rotationX
+            #end if
+
+            #if $rotationY:
+                --rotationY $rotationY
+            #end if
 
             #if $loops:
                 --loops '$loops'
@@ -102,6 +121,9 @@
             help="If given then only the region defined by --region and --region2 is plotted. The format is the same as --region"/>
         <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue="" checked="false" label="Plot the log1p of the matrix values (log(Hi-C contacts+1)). This option is recommended."/>
         <param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the log of the matrix values. (log(Hi-C contacts))"/>
+        <param argument="--fontSize" type="integer" optional="true" label="Font size" help="Fontsize in the plot for x and y axis."/>
+        <param argument="--rotationX" type="integer" optional="true" label="Rotate x-labels by degree" help="Rotation in degrees for the labels of x-axis."/>
+        <param argument="--rotationY" type="integer" optional="true" label="Rotate y-labels by degree" help="Rotation in degrees for the labels of y-axis."/>
 
         <expand macro="colormap" />
 
@@ -187,7 +209,7 @@
             <param name="image_file_format" value="svg" />
             <output name="outFileName" file="hicPlotMatrix/plot3_pca.svg" ftype="svg" compare="sim_size" delta="35000"/>
         </test>
-        
+
     </tests>
     <help><![CDATA[
 Contact matrix plot