diff profiler.xml @ 1:21d563d5f2b2 draft

Uploaded

--- a/profiler.xml	Sat Aug 03 13:42:12 2013 -0400
+++ b/profiler.xml	Mon Aug 05 10:09:51 2013 -0400
@@ -3,12 +3,16 @@
     creates a profile plot for a score associated to genomic regions
   </description>
   <requirements>
-    <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement>
+    <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement>
   </requirements>
   <command>
   profiler
+
+  ##ToDo
+  --numberOfProcessors 4
+
   --matrixFile $matrixFile
-  
+
   #if $output.showOutputSettings == "yes"
       #set newoutFileName=str($outFileName)+"."+str($output.outFileFormat)
       --outFileName $newoutFilename
@@ -24,8 +28,8 @@
         --outFileSortedRegions '$output.outFileSortedRegions'
       #end if
   #else
-  #set newoutFileName=str($outFileName)+".png"
-  --outFileName $newoutFileName
+    #set newoutFileName=str($outFileName)+".png"
+    --outFileName $newoutFileName
   #end if
   
   #if $scaleRegions.showScaleRegionsOpt == "yes":
@@ -47,16 +51,16 @@
     #if str($advancedOpt.plotTitle.value) != "None":
       --plotTitle '$advancedOpt.plotTitle'
     #end if
-      
+
     $advancedOpt.onePlotPerGroup
-    
+
     #if $advancedOpt.yMin:
       --yMin $advancedOpt.yMin
     #end if
     #if $advancedOpt.yMax:
       --yMax $advancedOpt.yMax
     #end if
-      
+
     --xAxisLabel '$advancedOpt.xAxisLabel'
     #if str($advancedOpt.yAxisLabel.value) != "None":
       --yAxisLabel '$advancedOpt.yAxisLabel'
@@ -64,7 +68,6 @@
   #end if
   ; mv $newoutFileName $outFileName
   </command>
-
   <inputs>
     <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>
     <conditional name="scaleRegions">
@@ -115,14 +118,12 @@
           <option value="sum">sum</option>
           <option value="std">std</option>
         </param>
-        
         <param name="plotHeight" type="integer" value="5" min="3" 
           label="Plot height" 
           help="Height in cm. The default for the plot height is 5 centimeters. The minimum value is 3 cm." />
         <param name="plotWidth" type="integer" value="8" min="1" 
           label="Plot width" 
           help="Width in cm. The default value is 8 centimeters. The minimum value is 1 cm." />
-        
         <param name="plotType" type="select" label="Plot type"
           help="For the summary plot (profile) only. The &quot;lines&quot; option will plot the profile line based on the average type selected. The &quot;fill&quot; option fills the region between zero and the profile curve. The fill in color is semi transparent to distinguish different profiles. The &quot;std&quot; option colors the region between the profile and the standard deviation of the data. As in the case of fill, a semi-transparent color is used. The option &quot;overlapped_lines&quot; plots each region values, one on top of the other; this option only works if &quot;one plot per proup&quot; is set.">
           <option value="lines" selected="true">lines</option>
@@ -134,10 +135,8 @@
         <param name="regionsLabel" type="text" value="genes" size="30" label="Labels for the regions plotted in the heatmap" help="If more than one region is being plotted a list of labels separated by comma and limited by quotes, is required. For example, &quot;label1, label2&quot;."/>
         <param name="plotTitle" type="text" value="" size="30" label="Title of the plot" help="Title of the plot, to be printed on top of the generated image. Leave blank for no title." />
         <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" label="Do one plot per group" help="When the region file contains groups separated by &quot;#&quot;, the default is to plot the averages for the distinct plots in one plot. If this option is set, each group will get its own plot, stacked on top of each other."/>
-
         <param name="yMin" type="float" value="" size="3" label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" optional="true"/>
         <param name="yMax" type="float" value="" size="3" label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" optional="true"/>
-
         <param name="xAxisLabel" type="text" value="gene distance (bp)" size="50" label="Description for the x-axis label" />
         <param name="yAxisLabel" type="text" value="" size="50" label="Description for the y-axis label for the top panel" />
       </when>
@@ -185,5 +184,4 @@
 .. _Fidel Ramirez: [e-mail]
 
   </help>
-  
 </tool>