# 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 - - - - - - - - - - - - - - - - - - - - -**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/ + + +