Mercurial > repos > bgruening > bedtools_test_bag

changeset 1:3b3e7774f51a draft

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Uploaded
author bgruening
date Tue, 08 Jan 2013 08:54:50 -0500
parents fa875e3c66c3
children 662c1741c22d
files bedtools-galaxy/bamToBed.xml bedtools-galaxy/coverageBed_counts.xml bedtools-galaxy/genomeCoverageBed_bedgraph.xml bedtools-galaxy/genomeCoverageBed_histogram.xml bedtools-galaxy/intersectBed.xml bedtools-galaxy/multiIntersectBed.xml bedtools-galaxy/sortBed.xml bedtools-galaxy/unionBedGraphs.xml
diffstat 8 files changed, 10 insertions(+), 49 deletions(-) [+]
line wrap: on
line diff
--- a/bedtools-galaxy/bamToBed.xml	Wed Jan 02 18:27:11 2013 -0500
+++ b/bedtools-galaxy/bamToBed.xml	Tue Jan 08 08:54:50 2013 -0500
@@ -51,16 +51,12 @@
 
 If creating a BEDPE output (see output formatting options), the BAM file should be sorted by query name.
 
-.. class:: warningmark
-
-This tool requires that `bedtools`__ has been installed on your system.
 
 ------
 
 This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__. If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__
 
     .. __: http://code.google.com/p/bedtools/
-    .. __: http://code.google.com/p/bedtools/
     .. __: http://cphg.virginia.edu/quinlan/
     .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short
 
--- a/bedtools-galaxy/coverageBed_counts.xml	Wed Jan 02 18:27:11 2013 -0500
+++ b/bedtools-galaxy/coverageBed_counts.xml	Tue Jan 08 08:54:50 2013 -0500
@@ -52,16 +52,12 @@
 
 The output file will be comprised of each interval from your original target BED file, plus an additional column indicating the number of intervals in your source file that overlapped that target interval.
 
-.. class:: warningmark
-
-This tool requires that `bedtools`__ has been installed on your system.
 
 ------
 
 This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__. If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__
 
     .. __: http://code.google.com/p/bedtools/
-    .. __: http://code.google.com/p/bedtools/
     .. __: http://cphg.virginia.edu/quinlan/
     .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short
 
--- a/bedtools-galaxy/genomeCoverageBed_bedgraph.xml	Wed Jan 02 18:27:11 2013 -0500
+++ b/bedtools-galaxy/genomeCoverageBed_bedgraph.xml	Tue Jan 08 08:54:50 2013 -0500
@@ -58,10 +58,6 @@
 
 The input BED or BAM file must be sorted by chromosome name (but doesn't necessarily have to be sorted by start position).
 
-.. class:: warningmark
-
-This tool requires that `bedtools`__ has been installed on your system.
-
 -----
 
 **Example 1**
@@ -110,7 +106,6 @@
 This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__. If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__
 
         .. __: http://code.google.com/p/bedtools/
-        .. __: http://code.google.com/p/bedtools/
         .. __: http://cphg.virginia.edu/quinlan/
         .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short
 </help>
--- a/bedtools-galaxy/genomeCoverageBed_histogram.xml	Wed Jan 02 18:27:11 2013 -0500
+++ b/bedtools-galaxy/genomeCoverageBed_histogram.xml	Tue Jan 08 08:54:50 2013 -0500
@@ -36,9 +36,6 @@
 
 ------
 
-.. class:: warningmark
-
-This tool requires that `bedtools`__ has been installed on your system.
 
 .. class:: infomark
 
@@ -71,7 +68,6 @@
 This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__. If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__
 
     .. __: http://code.google.com/p/bedtools/
-    .. __: http://code.google.com/p/bedtools/
     .. __: http://cphg.virginia.edu/quinlan/
     .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short
 
--- a/bedtools-galaxy/intersectBed.xml	Wed Jan 02 18:27:11 2013 -0500
+++ b/bedtools-galaxy/intersectBed.xml	Tue Jan 08 08:54:50 2013 -0500
@@ -28,7 +28,7 @@
     </command>
 
     <inputs>
-        <param format="bed,bam" name="inputA" type="data" label="BED or BAM file"/>
+        <param format="bed,bam,vcf,gff,gff3" name="inputA" type="data" label="BED or BAM file"/>
         <param format="bed" name="inputB" type="data" label="overlap intervals in this BED file?"/>
         
         <param name="strand" type="select" label="Calculate coverage based on">
@@ -73,26 +73,25 @@
 
 **What it does**
 
-This tool creates a new BAM alignment file based on alignments that overlap (or optionally, those that do not overlap) intervals in another BED file.  Example usage would be to cull a BAM file from an exome capture experiment to include on the "on-target" alignments. 
+It allows one to screen for overlaps between two sets of genomic features. Moreover, it allows one to have
+fine control as to how the intersections are reported. intersectBed works with both BED/GFF/VCF
+and BAM files as input.
+Example usage would be to cull a BAM file from an exome capture experiment to include on the "on-target" alignments. 
 
 .. class:: infomark
 
-Note that each BAM alignment is treated individually.  Therefore, if one end of a paired-end alignment overlaps an interval in the BED file, yet the other end does not, the output file will only include the overlapping end.
+Note that each BAM alignment is treated individually. Therefore, if one end of a paired-end alignment overlaps an interval in the BED file, yet the other end does not, the output file will only include the overlapping end.
 
 .. class:: infomark
 
 Note that a BAM alignment will be sent to the output file **once** even if it overlaps more than one interval in the BED file.
 
-.. class:: warningmark
-
-This tool requires that `bedtools`__ has been installed on your system.
 
 ------
 
 This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__. If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__
 
     .. __: http://code.google.com/p/bedtools/
-    .. __: http://code.google.com/p/bedtools/
     .. __: http://cphg.virginia.edu/quinlan/
     .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short
 
--- a/bedtools-galaxy/multiIntersectBed.xml	Wed Jan 02 18:27:11 2013 -0500
+++ b/bedtools-galaxy/multiIntersectBed.xml	Tue Jan 08 08:54:50 2013 -0500
@@ -114,9 +114,6 @@
 
 This tool requires that each BED file is reference-sorted (chrom, then start).
 
-.. class:: warningmark
-
-This tool requires that `bedtools`__ has been installed on your system.
 
 .. class:: infomark
 
@@ -198,7 +195,6 @@
 This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__. If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__
 
     .. __: http://code.google.com/p/bedtools/
-    .. __: http://code.google.com/p/bedtools/
     .. __: http://cphg.virginia.edu/quinlan/
     .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short
 
--- a/bedtools-galaxy/sortBed.xml	Wed Jan 02 18:27:11 2013 -0500
+++ b/bedtools-galaxy/sortBed.xml	Tue Jan 08 08:54:50 2013 -0500
@@ -34,33 +34,20 @@
 
 **What it does**
 
-This tool converts a BAM file to a BED file. The end coordinate is computed
-by inspecting the CIGAR string. The QNAME for the alignment is used as the 
-BED name field and, by default, the MAPQ is used as the BED score. 
-
-.. class:: infomark
-
-The "Report spliced BAM alignment..." option breaks BAM alignments with the "N" (splice) operator into distinct BED entries.  For example, using this option on a CIGAR such as 50M1000N50M would, by default, produce a single BED record that spans 1100bp.  However, using this option, it would create two separate BED records that are each 50bp in size and are separated by 1000bp (the size of the N operation).  This is important for RNA-seq and structural variation experiments.
+Sorts a feature file by chromosome and other criteria.
 
 
 .. class:: warningmark
 
-If using a custom BAM alignment TAG as  the BED score, note that this must be a numeric tag (e.g., type "i" as in NM:i:0).
-
-.. class:: warningmark
-
-If creating a BEDPE output (see output formatting options), the BAM file should be sorted by query name.
-
-.. class:: warningmark
-
-This tool requires that `bedtools`__ has been installed on your system.
+It should be noted that sortBed is merely a convenience utility, as the UNIX sort utility
+will sort BED files more quickly while using less memory. For example, UNIX sort will sort a BED file
+by chromosome then by start position in the following manner: sort -k 1,1 -k2,2 -n a.bed
 
 ------
 
 This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__. If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__
 
     .. __: http://code.google.com/p/bedtools/
-    .. __: http://code.google.com/p/bedtools/
     .. __: http://cphg.virginia.edu/quinlan/
     .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short
 
--- a/bedtools-galaxy/unionBedGraphs.xml	Wed Jan 02 18:27:11 2013 -0500
+++ b/bedtools-galaxy/unionBedGraphs.xml	Tue Jan 08 08:54:50 2013 -0500
@@ -116,9 +116,6 @@
 
 This tool requires that each BedGraph file is reference-sorted (chrom, then start) and contains non-overlapping intervals (within a given file).
 
-.. class:: warningmark
-
-This tool requires that `bedtools`__ has been installed on your system.
 
 ------
 
@@ -238,7 +235,6 @@
 This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__. If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__
 
     .. __: http://code.google.com/p/bedtools/
-    .. __: http://code.google.com/p/bedtools/
     .. __: http://cphg.virginia.edu/quinlan/
     .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short