Mercurial > repos > bgruening > deeptools_compute_matrix

diff computeMatrix.xml @ 1:de51aa03c9b9 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427
author bgruening
date Fri, 18 Dec 2015 08:01:48 -0500
parents f1db8b6a8743
children 2f2dd609644f
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line diff
--- a/computeMatrix.xml	Wed Dec 16 16:42:28 2015 -0500
+++ b/computeMatrix.xml	Fri Dec 18 08:01:48 2015 -0500
@@ -59,7 +59,7 @@
                 --sortRegions '$advancedOpt.sortRegions'
                 --sortUsing '$advancedOpt.sortUsing'
                 --averageTypeBins '$advancedOpt.averageTypeBins'
-                $advancedOpt.keepNAs
+                $advancedOpt.skipNAs
                 $advancedOpt.skipZeros
                 --binSize $advancedOpt.binSize
 
@@ -182,7 +182,12 @@
                     <option value="std">std</option>
                 </param>
 
-                <expand macro="keepNAs" />
+                <param name="missingDataAsZero" type="boolean" truevalue="--missingDataAsZero" falsevalue="" checked="False"
+                    label="Convert missing values to 0?."
+                    help="If set to 'yes', missing values (NAs) are converted to 0.
+                          The default is to ignore such cases, which will be
+                          depicted as black areas in the heatmap by default." />
+
                 <expand macro="skipZeros" />
 
                 <param name="minThreshold" type="float" optional="True"
@@ -219,7 +224,7 @@
             <param name="binSize" value="10" />
             <param name="sortUsing" value="sum" />
             <param name="averageTypeBins" value="sum" />
-            <param name="keepNAs" value="True" />
+            <param name="skipNAs" value="False" />
             <param name="beforeRegionStartLength" value="10" />
             <param name="afterRegionStartLength" value="10" />
             <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />