Mercurial > repos > aaronquinlan > bedtools
changeset 7:4e4b7c1a485c
Uploaded
| author | aaronquinlan |
|---|---|
| date | Wed, 07 Dec 2011 16:46:33 -0500 |
| parents | 81a5d327063f |
| children | 873a1f2dd665 |
| files | bedtools-galaxy/bedtools-galaxy/bamToBed.xml bedtools-galaxy/bedtools-galaxy/bedtools-galaxy/bamToBed.xml |
| diffstat | 2 files changed, 48 insertions(+), 48 deletions(-) [+] |
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--- a/bedtools-galaxy/bedtools-galaxy/bamToBed.xml Wed Dec 07 16:41:46 2011 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,48 +0,0 @@ -<tool id="bedtools_bamtobed" name="Convert from BAM to BED." version="2.14.4"> -<description></description> - -<requirements> - <requirement type="binary">bamToBed</requirement> -</requirements> - -<command> - bamToBed $option $ed_score -i '$input' > '$output' - #if str($tag): - -tag $tag - #end if -</command> - -<inputs> - <param format="bam" name="input" type="data" label="Input BAM file"/> - <param name="option" type="select" label="Output formatting options"> - <option value="">Create a 6-column BED file.</option> - <option value="-bed12">Create a full, 12-column "blocked" BED file.</option> - <option value="-bedpe">Create a paired-end, BEDPE format.</option> - </param> - <param name="split" type="boolean" label="Report spliced BAM alignments as separate BED entries." truevalue="-split" falsevalue="" checked="false"/> - <param name="ed_score" type="boolean" label="Use alignment's edit-distance for BED score" truevalue="-ed" falsevalue="" checked="false"/> - <param name="tag" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score"/> -</inputs> - -<outputs> - <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/> -</outputs> - -<help> - -**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. - ------- - - -This tool is part of the `BEDTools package`__ from the `Quinlan laboratory`__. - -.. __: http://code.google.com/p/bedtools/ -.. __: http://cphg.virginia.edu/quinlan/ - -</help> -</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bedtools-galaxy/bedtools-galaxy/bedtools-galaxy/bamToBed.xml Wed Dec 07 16:46:33 2011 -0500 @@ -0,0 +1,48 @@ +<tool id="bedtools_bamtobed" name="Convert from BAM to BED." version="2.14.4"> +<description></description> + +<requirements> + <requirement type="binary">bamToBed</requirement> +</requirements> + +<command> + bamToBed $option $ed_score -i '$input' > '$output' + #if str($tag): + -tag $tag + #end if +</command> + +<inputs> + <param format="bam" name="input" type="data" label="Input BAM file"/> + <param name="option" type="select" label="Output formatting options"> + <option value="">Create a 6-column BED file.</option> + <option value="-bed12">Create a full, 12-column "blocked" BED file.</option> + <option value="-bedpe">Create a paired-end, BEDPE format.</option> + </param> + <param name="split" type="boolean" label="Report spliced BAM alignments as separate BED entries." truevalue="-split" falsevalue="" checked="false"/> + <param name="ed_score" type="boolean" label="Use alignment's edit-distance for BED score" truevalue="-ed" falsevalue="" checked="false"/> + <param name="tag" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score"/> +</inputs> + +<outputs> + <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/> +</outputs> + +<help> + +**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. + +------ + + +This tool is part of the `BEDTools package`__ from the `Quinlan laboratory`__. + +.. __: http://code.google.com/p/bedtools/ +.. __: http://cphg.virginia.edu/quinlan/ + +</help> +</tool>