Mercurial > repos > xiaoyi-cao > annotatebed
changeset 0:0cba7d8f48ab draft
Uploaded
| author | xiaoyi-cao |
|---|---|
| date | Sun, 02 Dec 2012 12:11:45 -0500 |
| parents | |
| children | c3abf1788815 |
| files | ._annotateBed ._annotateBedWrapper.xml annotateBed annotateBedWrapper.xml |
| diffstat | 4 files changed, 46 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/annotateBed Sun Dec 02 12:11:45 2012 -0500 @@ -0,0 +1,2 @@ +#!/bin/sh +${0%/*}/bedtools annotate "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/annotateBedWrapper.xml Sun Dec 02 12:11:45 2012 -0500 @@ -0,0 +1,44 @@ +<tool id="annotateBed" name="annotateBed"> + + <description>TYPE_DESCRIPTION_HERE</description> + + <command interpreter="bash"> + names="" + inputfiles="" + #for $i, $s in enumerate($annotateColumn) + names=$names + ${s.colname} + " " + inputfiles=$inputfiles+ ${s.colfile} + " " + #end for + bedtools annotate $countflag -names $names -i $inputRegion -files $inputfiles + </command> + + <inputs> + + <param name="countflag" type="boolean" label="Use count to annotate" truevalue="-count" falsevalue="" /> + <param format="bed" name="inputRegion" type="data" label="The region to be annotated" /> + <repeat name="annotateColumn" title="Column"> + <param name="colname" type="text" label="Column name" /> + <param name="colfile" type="data" format="bed" label="BED file to annotate for the column" /> + </repeat> + + </inputs> + + <outputs> + + <data format="bed" name="output" /> + + </outputs> + +<help> + +.. class:: infomark + +IMPORTANT INFORMATION + +---- + +WRITE HELP HERE + +</help> + +</tool> \ No newline at end of file