diff computeGCBias.xml @ 18:5ea8782d650c draft

Uploaded

--- a/computeGCBias.xml	Sat Dec 21 14:26:06 2013 -0500
+++ b/computeGCBias.xml	Mon Feb 03 13:44:35 2014 -0500
@@ -1,8 +1,9 @@
-<tool id="deeptools_computeGCBias" name="computeGCBias" version="1.0.2">
+<tool id="deeptools_computeGCBias" name="computeGCBias" version="1.0.3">
     <description>to see whether your samples should be normalized for GC bias</description>
     <expand macro="requirements" />
     <expand macro="stdio" />
     <macros>
+        <token name="@BINARY@">computeGCBias</token>
         <import>deepTools_macros.xml</import>
     </macros>
     <command>
@@ -24,10 +25,11 @@
                 --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
             #end if
 
+            #if str(region).strip() != '':
+                --region 'region'
+            #end if
+
             #if $advancedOpt.showAdvancedOpt == "yes":
-                #if str($advancedOpt.region.value) != '':
-                    --region '$advancedOpt.region'
-                #end if
 
                 --sampleSize '$advancedOpt.sampleSize'
                 --regionSize '$advancedOpt.regionSize'
@@ -56,6 +58,9 @@
         <param name="fragmentLength" type="integer" value="300" min="1"
             label="Fragment length used for the sequencing"
             help ="If paired-end reads are used, the fragment length is computed from the BAM file."/>
+
+        <expand macro="region_limit_operation" />
+
         <conditional name="advancedOpt">
             <param name="showAdvancedOpt" type="select" label="Show advanced options" >
                 <option value="no" selected="true">no</option>
@@ -63,10 +68,6 @@
             </param>
             <when value="no" />
             <when value="yes">
-                <param name="region" type="text" value=""
-                    label="Region of the genome to limit the operation to"
-                    help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" />
-
                 <param name="sampleSize" type="integer" value="50000000" min="1"
                     label="Number of sampling points to be considered" />
 
@@ -131,6 +132,11 @@
 .. image:: $PATH_TO_IMAGES/QC_GCplots_input.png
 
 
+You can find more details in the `computeGCBias wiki`_.
+
+.. _computeGCBias wiki: https://github.com/fidelram/deepTools/wiki/QC#wiki-computeGCbias
+
+
 **Output files**:
 
 - Diagnostic plot
@@ -145,8 +151,6 @@
 
 -----
 
-.. class:: infomark
-
 @REFERENCES@
 
     </help>