diff profiler.xml @ 6:c5847db0cb41 draft

Uploaded

--- a/profiler.xml	Tue Aug 06 08:20:47 2013 -0400
+++ b/profiler.xml	Wed Aug 14 07:18:18 2013 -0400
@@ -1,9 +1,10 @@
-<tool id="dt_profiler" name="profiler" version="1.0">
+<tool id="deeptools_profiler" name="profiler" version="1.0">
   <description>
     creates a profile plot for a score associated to genomic regions
   </description>
   <requirements>
-    <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement>
+    <requirement type="package" version="1.5.1_df852fa1ef13251a17274ee18fbf919fbc515079">deepTools</requirement>
+    <requirement type="package" >deepTools</requirement>
   </requirements>
   <command>
   profiler
@@ -13,16 +14,16 @@
   #if $output.showOutputSettings == "yes"
       #set newoutFileName = str($outFileName)+"."+str($output.outFileFormat)
       --outFileName $newoutFileName
-      #if $output.outFileNameData:
-        --outFileNameData '$output.outFileNameData' 
+      #if $output.saveData:
+        --outFileNameData '$outFileNameData' 
       #end if
 
-      #if $output.outFileNameMatrix:
-      --outFileNameMatrix '$output.outFileNameMatrix'
+      #if $output.saveMatrix:
+      --outFileNameMatrix '$outFileNameMatrix'
       #end if
-      
-      #if $output.outFileSortedRegions:
-        --outFileSortedRegions '$output.outFileSortedRegions'
+
+      #if $output.saveSortedRegions:
+        --outFileSortedRegions '$outFileSortedRegions'
       #end if
   #else
     #set newoutFileName = str($outFileName)+".png"
@@ -32,7 +33,6 @@
   #if $scaleRegions.showScaleRegionsOpt == "yes":
     --startLabel $scaleRegions.startLabel
     --endLabel $scaleRegions.endLabel
-    --refPointLabel $scaleRegions.refPointLabel
   #end if
   
   #if $advancedOpt.showAdvancedOpt == "yes"
@@ -76,7 +76,6 @@
         <when value="yes">
             <param name="startLabel" type="text" value="TSS" size="10" label="Label for the region start" help ="[only for scale-regions mode] Label shown in the plot for the start of the region. Default is TSS (transcription start site), but could be changed to anything, e.g. &quot;peak start&quot;." />
             <param name="endLabel" type="text" value="TES" size="10" label="Label for the region end" help="[only for scale-regions mode] Label shown in the plot for the region end. Default is TES (transcription end site)."/>
-            <param name="refPointLabel" type="text" value="TSS" size="10" label="Reference point label" help ="[only for scale-regions mode] Label shown in the plot for the reference-point. Default is the same as the reference point selected (e.g. TSS), but could be anything, e.g. &quot;peak start&quot; etc." />
         </when>
     </conditional>
 
@@ -141,12 +140,12 @@
   </inputs>
   <outputs>
     <data format="png" name="outFileName" label="${tool.name} image">
-    <change_format>
-        <when input="output.outFileFormat" value="pdf" format="pdf" />
-        <when input="output.outFileFormat" value="svg" format="svg" />
-        <when input="output.outFileFormat" value="eps" format="eps" />
-        <when input="output.outFileFormat" value="emf" format="emf" />
-    </change_format>
+        <change_format>
+            <when input="output.outFileFormat" value="pdf" format="pdf" />
+            <when input="output.outFileFormat" value="svg" format="svg" />
+            <when input="output.outFileFormat" value="eps" format="eps" />
+            <when input="output.outFileFormat" value="emf" format="emf" />
+        </change_format>
     </data>
     <data format="tabular" name="outFileNameData" label="${tool.name} raw plot data">
       <filter>(output['showOutputSettings'] == 'yes' and output['saveData'] == True)</filter>
@@ -164,21 +163,20 @@
 
 This tool creates a profile plot for a score associated to genomic regions.
 Typically, these regions are genes, but any other regions defined in a BED or
-GFF format will work. A preprocessed matrix generated by the tool
+INTERVAL format will work. A preprocessed matrix generated by the tool
 computeMatrix is required.
 
 -----
 
 .. class:: infomark
 
-If you would like to give us feedback or you run into any trouble, please sent an email to [e-mail]
+If you would like to give us feedback or you run into any trouble, please send an email to [e-mail]
 
 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
 
 
 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
-.. _Fidel Ramirez: [e-mail]
 
   </help>
 </tool>