diff bamCoverage.xml @ 18:5ea8782d650c draft

Uploaded

--- a/bamCoverage.xml	Sat Dec 21 14:26:06 2013 -0500
+++ b/bamCoverage.xml	Mon Feb 03 13:44:35 2014 -0500
@@ -1,8 +1,9 @@
-<tool id="deeptools_bamCoverage" name="bamCoverage" version="1.0.2">
+<tool id="deeptools_bamCoverage" name="bamCoverage" version="1.0.3">
     <description> generates a coverage bigWig file from a given BAM file.  Multiple options are available to count reads and normalize coverage. (bam2bigwig)</description>
     <expand macro="requirements" />
     <expand macro="stdio" />
     <macros>
+        <token name="@BINARY@">bamCoverage</token>
         <import>deepTools_macros.xml</import>
     </macros>
     <command>
@@ -21,19 +22,24 @@
         #if $scaling.type=='rpkm':
             --normalizeUsingRPKM
         #elif $scaling.type=='1x':
-            --normalizeTo1x $scaling.normalizeTo1x
+            #if $scaling.effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
+                --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize
+            #else:
+                --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize_opt
+            #end if
         #elif $scaling.type=='own':
             --scaleFactor $scaling.scaleFactor
         #end if
 
+        #if str(region).strip() != '':
+            --region 'region'
+        #end if
+
         #if $advancedOpt.showAdvancedOpt == "yes":
             #if $advancedOpt.smoothLength:
                 --smoothLength '$advancedOpt.smoothLength'
             #end if
 
-            #if str($advancedOpt.region.value) != '':
-                --region '$advancedOpt.region'
-            #end if
             $advancedOpt.doNotExtendPairedEnds
             $advancedOpt.ignoreDuplicates
 
@@ -70,9 +76,7 @@
             <when value="rpkm"/>
             <when value="no"/>
             <when value="1x">
-                <param name="normalizeTo1x" type="integer" value="2150570000"
-                    label="Genome size"
-                    help ="Enter the genome size to normalize the reads counts. Sequencing depth is defined as the total number of mapped reads * fragment length / effective genome size. To use this option, the effective genome size has to be given. Common values are: mm9: 2150570000, hg19:2451960000, dm3:121400000 and ce10:93260000."/>
+                <expand macro="effectiveGenomeSize" />
             </when>
             <when value="own">
                 <param name="scaleFactor" type="float" value="1" size="3" 
@@ -85,6 +89,8 @@
             <option value="bedgraph">bedgraph</option>
         </param>
 
+        <expand macro="region_limit_operation" />
+
         <conditional name="advancedOpt">
             <param name="showAdvancedOpt" type="select" label="Show advanced options" >
                 <option value="no" selected="true">no</option>
@@ -96,10 +102,6 @@
                     label="Smooth values using the following length (in bp)"
                     help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
 
-                <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="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
                     label="Do not extend paired ends"
                     help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/>
@@ -140,14 +142,17 @@
 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png
 
 
+You can find more details in the `bamCoverage wiki`_.
+
+.. _bamCoverage wiki: https://github.com/fidelram/deepTools/wiki/Normalizations#wiki-bamCoverage
+
+
 **Output files**:
 
 - coverage file either in bigWig or bedGraph format
 
 -----
 
-.. class:: infomark
-
 @REFERENCES@
 
     </help>