diff bamCoverage.xml @ 6:c5847db0cb41 draft

Uploaded

--- a/bamCoverage.xml	Tue Aug 06 08:20:47 2013 -0400
+++ b/bamCoverage.xml	Wed Aug 14 07:18:18 2013 -0400
@@ -1,9 +1,10 @@
-<tool id="bamCoverage" name="bamCoverage" version="1.0">
-  <description>Given a BAM file, generates a coverage bigwig file.  Multiple options available to count reads and normalize coverage.</description>
+<tool id="deeptools_bamCoverage" name="bamCoverage" version="1.0">
+  <description> generates a coverage bigWig file from a given BAM file.  Multiple options are available to count reads and normalize coverage.</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" version="0.1">ucsc_tools</requirement>
     <requirement type="package" version="1.7.1">numpy</requirement>
+    <requirement type="package" >deepTools</requirement>
   </requirements>
   <command>
   bamCoverage
@@ -26,7 +27,11 @@
   #elif $scaling.type=='own':
     --scaleFactor $scaling.scaleFactor
   #end if
-  
+
+  ##if str($ignoreForNormalization).strip() != '':
+  ##  --ignoreForNormalization $ignoreForNormalization
+  ##end if
+
   #if $advancedOpt.showAdvancedOpt == "yes":
     #if $advancedOpt.smoothLength:
       --smoothLength '$advancedOpt.smoothLength'
@@ -47,7 +52,7 @@
 
   <inputs>
     <param name="bamInput" format="bam" type="data" label="Input BAM file"
-       help="The BAM file must be sorted and indexed."/>
+       help="The BAM file must be sorted."/>
 
     <param name="fragmentLength" type="integer" value="300" min="1"
        label="Length of the average fragment size"
@@ -77,6 +82,13 @@
         </when>
     </conditional>
 
+    <!--
+    Not yet supported.
+    <param name="ignoreForNormalization" type="text" value="" size="50"
+        label="regions that should be excluded for calculating the scaling factor"
+        help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor. For example, if you know some regions that you suspect to be present more often in your sample's genome than in the reference genome that will therefore accumulate reads (CNV). Another typical example is the single X chromosome in male samples that should be scaled separately from the diploid autosomes. For example chrX,chrY,chr3. or chr10:12220-128932" />
+    -->
+
     <param name="outFileFormat" type="select" label="Coverage file format">
         <option value="bigwig" selected="true">bigwig</option>
         <option value="bedgraph">bedgraph</option>
@@ -107,7 +119,7 @@
 
           <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
             label="Minimum mapping quality"
-            help= "If set, only reads that have a mapping quality score higher than the given value are considered"/>
+            help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
         </when>
     </conditional>
   </inputs>
@@ -129,14 +141,13 @@
 
 .. 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>