Mercurial > repos > xiaoyi-cao > annotatebed

comparison annotateBedWrapper.xml @ 2:21a126fcfd13 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Test2
author xiaoyi-cao
date Sun, 02 Dec 2012 14:38:33 -0500
parents 0cba7d8f48ab
children 37d0c1ec2c87
comparison
equal deleted inserted replaced
1:c3abf1788815 2:21a126fcfd13
1 <tool id="annotateBed" name="annotateBed"> 1 <tool id="annotateBed" name="annotateBed">
2 2
3 <description>TYPE_DESCRIPTION_HERE</description> 3 <description>TYPE_DESCRIPTION_HERE</description>
4 4
5 <command interpreter="bash"> 5 <command>
6 names="" 6 bedtools annotate
7 inputfiles="" 7 $countflag
8 #for $i, $s in enumerate($annotateColumn) 8 -i '$inputRegion'
9 names=$names + ${s.colname} + " " 9 -names
10 inputfiles=$inputfiles+ ${s.colfile} + " " 10 #for $s in enumerate($annotateColumn)
11 ${s.colname}
11 #end for 12 #end for
12 bedtools annotate $countflag -names $names -i $inputRegion -files $inputfiles 13 -files
14 #for $s in enumerate($annotateColumn)
15 ${s.colfile}
16 #end for
17 &gt; '$output'
13 </command> 18 </command>
14 19
15 <inputs> 20 <inputs>
16 21
17 <param name="countflag" type="boolean" label="Use count to annotate" truevalue="-count" falsevalue="" /> 22 <param name="countflag" type="boolean" label="Use count to annotate" truevalue="-count" falsevalue="" />
20 <param name="colname" type="text" label="Column name" /> 25 <param name="colname" type="text" label="Column name" />
21 <param name="colfile" type="data" format="bed" label="BED file to annotate for the column" /> 26 <param name="colfile" type="data" format="bed" label="BED file to annotate for the column" />
22 </repeat> 27 </repeat>
23 28
24 </inputs> 29 </inputs>
25
26 <outputs> 30 <outputs>
27 31 <data format="bed" name="output" metadata_source="input" label="${inputRegion.name} annotated" />
28 <data format="bed" name="output" />
29
30 </outputs> 32 </outputs>
31 33
32 <help> 34 <help>
33 35
34 .. class:: infomark 36 .. class:: infomark