Mercurial > repos > xuebing > bowtie_to_bed
changeset 0:611d7bc58c12
Uploaded
| author | xuebing |
|---|---|
| date | Sat, 31 Mar 2012 22:56:42 -0400 |
| parents | |
| children | 7cce5b64ee41 |
| files | bowtie_to_bed.xml |
| diffstat | 1 files changed, 44 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bowtie_to_bed.xml Sat Mar 31 22:56:42 2012 -0400 @@ -0,0 +1,44 @@ +<tool id="bowtie_to_bed" name="bowtie-to-bed"> + <description> converter</description> + <command interpreter="perl">bowtie_to_bed.pl $input $out_file1 $extendLength </command> + <inputs> + <param name="input" format="txt" type="data" label="Bowtie map result file"/> + <param name="extendLength" size="10" type="integer" value="200" label="Extend 3 primer (bp)"/> + </inputs> + <outputs> + <data format="bed" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="input" value="test.map" ftype="TXT"/> + <param name="extendLength" value="200"/> + <output name="out_file1" file="testmap.bed"/> + </test> + </tests> + <help> + + +**What it does** + +This tool converts bowtie output map format file to bed format, with the option to extend the 3 primer end. + +- Sequence and quality information is lost after conversion +- The output contains a track name at the first row + +----- + +**Example** + +Converting the following bowtie mapped reads:: + + SRR073078.2 HWUSI-EAS465_8_1_1_524 length=36 - chr2 112499209 AGTGTGACTGCATCTCTTCCTTCGTGGGGCTNCAGT ... + SRR073078.3 HWUSI-EAS465_8_1_1_1054 length=36 + chr17 75877120 CCACNCCTCCTTTCAAAACACACTGCCAGGTGCGTC ... + +will result in:: + + track name=/home/xuebing/Research/galaxy/galaxy-dist/database/files/000/dataset_5.dat itemRgb=On + chr2 112499109 112499245 SRR073078.2-HWUSI-EAS465_8_1_1_524-length=36 1 - 112499209 112499245 0,255,0 + chr17 75877120 75877256 SRR073078.3-HWUSI-EAS465_8_1_1_1054-length=36 1 + 75877120 75877156 255,0,0 + + </help> +</tool>