diff coverageBed.xml @ 11:7308cc546a36 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811

--- a/coverageBed.xml	Mon Oct 03 07:36:08 2016 -0400
+++ b/coverageBed.xml	Mon Oct 17 10:13:35 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.1">
+<tool id="bedtools_coveragebed" name="Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@.0">
     <description>of features in file B on the features in file A (bedtools coverage)</description>
     <macros>
         <import>macros.xml</import>
@@ -24,7 +24,7 @@
         <param format="bam,bed,gff,gff3,vcf" name="inputA" type="data" label="File A (on which coverage is calculated)" help="BAM/BED/GFF/VCF format" />
         <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data" multiple="true" label="File(s) B (for which coverage is calculated)" help="BAM/BED/GFF/VCF format" />
         <expand macro="split" />
-        <param name="strandedness" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false" 
+        <param name="strandedness" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false"
             help="Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand (-s)"/>
         <param name="d" type="boolean" checked="false" truevalue="-d" falsevalue=""
             label="Report the depth at each position in each A feature"
@@ -47,10 +47,10 @@
 <![CDATA[
 **What it does**
 
-`bedtools coverage`_ computes both the *depth* and *breadth* of coverage of features in 
-file B on the features in file A. For example, ``bedtools coverage`` can compute the coverage of sequence alignments 
-(file B) across 1 kilobase (arbitrary) windows (file A) tiling a genome of interest. 
-One advantage that ``bedtools coverage`` offers is that it not only *counts* the number of features that 
+`bedtools coverage`_ computes both the *depth* and *breadth* of coverage of features in
+file B on the features in file A. For example, ``bedtools coverage`` can compute the coverage of sequence alignments
+(file B) across 1 kilobase (arbitrary) windows (file A) tiling a genome of interest.
+One advantage that ``bedtools coverage`` offers is that it not only *counts* the number of features that
 overlap an interval in file A, it also computes the fraction of bases in the interval in A that were overlapped by one or more features.
 Thus, ``bedtools coverage`` also computes the *breadth* of coverage for each interval in A.