Mercurial > repos > aaronquinlan > bedtools
changeset 2:f2270e47bda1
Uploaded
author | aaronquinlan |
---|---|
date | Wed, 07 Dec 2011 13:28:53 -0500 |
parents | 52830b3f342a |
children | 4e5b6f0c6e70 |
files | bedtools-galaxy/bedtools-galaxy/bamToBed.xml bedtools-galaxy/galaxy_configs/tool_conf.xml bedtools-galaxy/galaxy_configs/tools/bamToBed.xml bedtools-galaxy/suite_config.xml |
diffstat | 4 files changed, 75 insertions(+), 92 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bedtools-galaxy/bedtools-galaxy/bamToBed.xml Wed Dec 07 13:28:53 2011 -0500 @@ -0,0 +1,75 @@ +<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. + +------- + +**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. +<!-- + -color An R,G,B string for the color used with BED12 format. + Default is (255,0,0). + + -cigar Add the CIGAR string to the BED entry as a 7th column. +--> + +------ + + +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>
--- a/bedtools-galaxy/galaxy_configs/tool_conf.xml Sat Nov 19 16:22:54 2011 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -<?xml version="1.0"?> -<toolbox> - - <label text="BEDTools 2.14.1" id="bedtools" /> - - <section name="Genome Arithmetic Tools" id="bedtools_ga"> - <tool file="bedtools/galaxy_configs/tools/bamToBed.xml"/> - </section> - -</toolbox> \ No newline at end of file
--- a/bedtools-galaxy/galaxy_configs/tools/bamToBed.xml Sat Nov 19 16:22:54 2011 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,71 +0,0 @@ -<tool id="bedtools_bamtobed" name="Convert from BAM to BED." version="2.14.4"> -<description></description> - -<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. - -------- - -**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. -<!-- - -color An R,G,B string for the color used with BED12 format. - Default is (255,0,0). - - -cigar Add the CIGAR string to the BED entry as a 7th column. ---> - ------- - - -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>
--- a/bedtools-galaxy/suite_config.xml Sat Nov 19 16:22:54 2011 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,11 +0,0 @@ -<suite id="bedtools_suite" name="bedtools" version="2.14.4"> - - <description> - bedtools: A flexible toolset for genome arithmetic and analysis. - </description> - - <tool id="bedtools_bamtobed" name="Upload File" version="1.1.2"> - <description>from your computer</description> - </tool> - -</suite> \ No newline at end of file