# HG changeset patch
# User aaronquinlan
# Date 1323283049 18000
# Node ID 4e5b6f0c6e7063533365520f120d562578b978e3
# Parent f2270e47bda180c6757af9a4e0ca1d1f514aa065
Uploaded
diff -r f2270e47bda1 -r 4e5b6f0c6e70 bedtools-galaxy/bedtools-galaxy/bamToBed.xml
--- a/bedtools-galaxy/bedtools-galaxy/bamToBed.xml Wed Dec 07 13:28:53 2011 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,75 +0,0 @@
-
-
-
-
- bamToBed
-
-
-
- bamToBed $option $ed_score -i '$input' > '$output'
- #if str($tag):
- -tag $tag
- #end if
-
-
-
-
-
-
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-
-
-
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-
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-
-
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-**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.
-
--------
-
-**Options**::
-
- -bedpe Write BEDPE format.
- - Requires BAM to be grouped or sorted by query.
-
- -bed12 Write "blocked" BED format (aka "BED12").
- http://genome-test.cse.ucsc.edu/FAQ/FAQformat#format1
-
- -split Report "split" BAM alignments as separate BED entries.
-
- -ed Use BAM edit distance (NM tag) for BED score.
- * Default for BED is to use mapping quality.
- * Default for BEDPE is to use the minimum of the two mapping qualities for the pair.
- * When -ed is used with -bedpe, the total edit distance from the two mates is reported.
-
- -tag Use other NUMERIC BAM alignment tag for BED score.
- * Default for BED is to use mapping quality.
- * Disallowed with BEDPE output.
-
-
-------
-
-
-This tool is part of the `BEDTools package`__ from the `Quinlan laboratory`__.
-
-.. __: http://code.google.com/p/bedtools/
-.. __: http://cphg.virginia.edu/quinlan/
-
-
-
diff -r f2270e47bda1 -r 4e5b6f0c6e70 bedtools-galaxy/bedtools-galaxy/bedtools-galaxy/bamToBed.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bedtools-galaxy/bedtools-galaxy/bedtools-galaxy/bamToBed.xml Wed Dec 07 13:37:29 2011 -0500
@@ -0,0 +1,75 @@
+
+
+
+
+ bamToBed
+
+
+
+ bamToBed $option $ed_score -i '$input' > '$output'
+ #if str($tag):
+ -tag $tag
+ #end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+**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.
+
+-------
+
+**Options**::
+
+ -bedpe Write BEDPE format.
+ - Requires BAM to be grouped or sorted by query.
+
+ -bed12 Write "blocked" BED format (aka "BED12").
+ http://genome-test.cse.ucsc.edu/FAQ/FAQformat#format1
+
+ -split Report "split" BAM alignments as separate BED entries.
+
+ -ed Use BAM edit distance (NM tag) for BED score.
+ * Default for BED is to use mapping quality.
+ * Default for BEDPE is to use the minimum of the two mapping qualities for the pair.
+ * When -ed is used with -bedpe, the total edit distance from the two mates is reported.
+
+ -tag Use other NUMERIC BAM alignment tag for BED score.
+ * Default for BED is to use mapping quality.
+ * Disallowed with BEDPE output.
+
+
+------
+
+
+This tool is part of the `BEDTools package`__ from the `Quinlan laboratory`__.
+
+.. __: http://code.google.com/p/bedtools/
+.. __: http://cphg.virginia.edu/quinlan/
+
+
+