annotate annotateBedWrapper.xml @ 1:c3abf1788815 draft

Deleted selected files
author xiaoyi-cao
date Sun, 02 Dec 2012 14:37:51 -0500
parents 0cba7d8f48ab
children 21a126fcfd13
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
1 <tool id="annotateBed" name="annotateBed">
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
2
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
3 <description>TYPE_DESCRIPTION_HERE</description>
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
4
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
5 <command interpreter="bash">
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
6 names=""
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
7 inputfiles=""
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
8 #for $i, $s in enumerate($annotateColumn)
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
9 names=$names + ${s.colname} + " "
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
10 inputfiles=$inputfiles+ ${s.colfile} + " "
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
11 #end for
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
12 bedtools annotate $countflag -names $names -i $inputRegion -files $inputfiles
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
13 </command>
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
14
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
15 <inputs>
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
16
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
17 <param name="countflag" type="boolean" label="Use count to annotate" truevalue="-count" falsevalue="" />
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
18 <param format="bed" name="inputRegion" type="data" label="The region to be annotated" />
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
19 <repeat name="annotateColumn" title="Column">
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
20 <param name="colname" type="text" label="Column name" />
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
21 <param name="colfile" type="data" format="bed" label="BED file to annotate for the column" />
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
22 </repeat>
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
23
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
24 </inputs>
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
25
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
26 <outputs>
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
27
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
28 <data format="bed" name="output" />
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
29
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
30 </outputs>
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
31
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
32 <help>
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
33
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
34 .. class:: infomark
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
35
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
36 IMPORTANT INFORMATION
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
37
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
38 ----
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
39
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
40 WRITE HELP HERE
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
41
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
42 </help>
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
43
0cba7d8f48ab Uploaded
xiaoyi-cao
parents:
diff changeset
44 </tool>