diff computeMatrix.xml @ 3:a842285199d9 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2e8510e4f4015f51f7726de5697ba2de9b4e2f4c

--- a/computeMatrix.xml	Thu Feb 18 11:53:52 2016 -0500
+++ b/computeMatrix.xml	Wed Mar 09 18:33:21 2016 -0500
@@ -51,7 +51,12 @@
                 #if $mode.regionStartLength.regionStartLength_select == "yes":
                     --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength
                     --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength
+
+                    --unscaled5prime $mode.regionStartLength.unscaled5prime
+                    --unscaled3prime $mode.regionStartLength.unscaled3prime
+
                 #end if
+
             #end if
 
             #if $advancedOpt.showAdvancedOpt == "yes":
@@ -71,7 +76,6 @@
                 #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '':
                     --scale $advancedOpt.scale
                 #end if
-
             #end if
 ]]>
     </command>
@@ -118,6 +122,14 @@
                             label="Distance downstream of the region end position"
                             help="If the regions are genes, this would be the
                             distance downstream of the transcription end site."/>
+                        <param argument="--unscaled5prime" type="integer" min="0" value="0"
+                            label="Number of bases within the gene body at the 5-prime end to exclude from scaling."
+                            help="By default, each region is scaled to a given length (see the --regionBodyLength
+                             option). In some cases it is useful to look at unscaled signals around region boundaries, so this
+                             setting specifies the number of unscaled bases on the 5-prime end of each boundary." />
+                        <param argument="--unscaled3prime" type="integer" min="0" value="0"
+                            label="Number of bases within the gene body at the 3-prime end to exclude from scaling."
+                            help="As with --unscaled5prime, but for the 3-prime end." />
                     </when>
                 </conditional>
             </when>
@@ -202,9 +214,6 @@
         <expand macro="output_graphic_outputs" />
         <expand macro="output_save_matrix_values" />
     </outputs>
-    <!--
-    computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1
-    -->
     <tests>
         <test>
             <param name="regionsFile" value="computeMatrix1.bed" ftype="bed" />