diff bamFingerprint.xml @ 18:5ea8782d650c draft

Uploaded

--- a/bamFingerprint.xml	Sat Dec 21 14:26:06 2013 -0500
+++ b/bamFingerprint.xml	Mon Feb 03 13:44:35 2014 -0500
@@ -1,8 +1,9 @@
-<tool id="deeptools_bamFingerprint" name="bamFingerprint" version="1.0.2">
+<tool id="deeptools_bamFingerprint" name="bamFingerprint" version="1.0.3">
     <description>plots profiles of BAM files; useful for assesing ChIP signal strength</description>
     <expand macro="requirements" />
     <expand macro="stdio" />
     <macros>
+        <token name="@BINARY@">bamFingerprint</token>
         <import>deepTools_macros.xml</import>
     </macros>
     <command>
@@ -29,12 +30,11 @@
         --plotFileFormat 'png'
       #end if
 
+      #if str(region).strip() != '':
+          --region 'region'
+      #end if
+
       #if $advancedOpt.showAdvancedOpt == "yes":
-        
-        #if str($advancedOpt.region.value) != '':
-          --region '$advancedOpt.region'
-        #end if
-
         --binSize '$advancedOpt.binSize'
         --numberOfSamples '$advancedOpt.numberOfSamples'
 
@@ -53,8 +53,12 @@
     <inputs>
         <expand macro="multiple_input_bams" />
 
+
         <param name="fragmentLength" type="integer" value="200" min="1"
            label="Length of the average fragment size"/>
+
+        <expand macro="region_limit_operation" />
+
         <conditional name="advancedOpt">
             <param name="showAdvancedOpt" type="select" label="Show advanced options" >
                 <option value="no" selected="true">no</option>
@@ -62,10 +66,6 @@
             </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="binSize" type="integer" value="10000" min="1" 
                    label="Bin size in bp"
                    help="Length in base pairs for a window used to sample the genome."/>
@@ -133,6 +133,11 @@
 .. image:: $PATH_TO_IMAGES/QC_fingerprint.png
 
 
+You can find more details in the `bamFingerprint wiki`_.
+
+.. _bamFingerprint wiki: https://github.com/fidelram/deepTools/wiki/QC#wiki-bamFingerprint
+
+
 **Output files**:
 
 - Diagnostic plot
@@ -140,8 +145,6 @@
 
 -----
 
-.. class:: infomark
-
 @REFERENCES@
 
     </help>