diff computeGCBias.xml @ 65:9bee2c86eeb1 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty

--- a/computeGCBias.xml	Sun Mar 22 13:02:33 2015 -0400
+++ b/computeGCBias.xml	Mon May 25 05:16:10 2015 -0400
@@ -1,11 +1,10 @@
 <tool id="deeptools_computeGCBias" name="computeGCBias" version="@WRAPPER_VERSION@.0">
     <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>
+    <expand macro="requirements" />
     <command>
 <![CDATA[
         ln -s $bamInput local_bamInput.bam;
@@ -31,7 +30,6 @@
             #end if
 
             #if $advancedOpt.showAdvancedOpt == "yes":
-
                 --sampleSize '$advancedOpt.sampleSize'
                 --regionSize '$advancedOpt.regionSize'
 
@@ -70,10 +68,17 @@
                     label="Number of sampling points to be considered" help="(--sampleSize)" />
                 <param name="regionSize" type="integer" value="300" min="1"
                     label="Region size"
-                    help ="To plot the reads per GC over a region, the size of the region is required (see below for more details of the mthod). By default, the bin size is set to 300 bp, which is close to the standard fragment size many sequencing applications. However, if the depth of sequencing is low, a larger bin size will be required, otherwise many bins will not overlap with any read. (--regionSize)"/>
+                    help ="To plot the reads per GC over a region, the size of the region is
+                    required (see below for more details of the mthod). By default, the bin size
+                    is set to 300 bp, which is close to the standard fragment size many sequencing
+                    applications. However, if the depth of sequencing is low, a larger bin size will
+                    be required, otherwise many bins will not overlap with any read. (--regionSize)"/>
                 <param name="filterOut" type="data" format="bed" optional="true"
                     label="BED file containing genomic regions to be excluded from the estimation of the correction"
-                    help="Such regions  usually contain repetitive regions and peaks that if included will bias the correction. It is recommended to filter out known repetitive regions if multi-reads (reads that map to more than one genomic position) were excluded. In the case of ChIP-seq data, it is recommended to first use a peak caller to identify and filter out the identified peaks. (--filterOut)" />
+                    help="Such regions  usually contain repetitive regions and peaks that if included will
+                    bias the correction. It is recommended to filter out known repetitive regions if multi-reads
+                    (reads that map to more than one genomic position) were excluded. In the case of ChIP-seq data,
+                    it is recommended to first use a peak caller to identify and filter out the identified peaks. (--filterOut)" />
                 <param name="extraSampling" type="data" format="bed" optional="true"
                     label="BED file containing genomic regions for which extra sampling is required because they are underrepresented in the genome"
                     help="(--extraSampling)" />