Mercurial > repos > yqiancolumbia > ctk_test
annotate bedExt.xml @ 0:0475e4175855 draft default tip
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
author | yqiancolumbia |
---|---|
date | Mon, 30 Apr 2018 05:25:11 -0400 |
parents | |
children |
rev | line source |
---|---|
0
0475e4175855
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
yqiancolumbia
parents:
diff
changeset
|
1 <tool id="bedExt" name="Get the position before the start site"> |
0475e4175855
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
yqiancolumbia
parents:
diff
changeset
|
2 <description>as a potential cross link site that causes truncation</description> |
0475e4175855
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
yqiancolumbia
parents:
diff
changeset
|
3 <command interpreter="perl"> |
0475e4175855
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
yqiancolumbia
parents:
diff
changeset
|
4 /home/galaxy/tools/CTK/bedExt.pl -n $NeighborRegion -l $LeftExtension -r $RightExtension -v $input $output |
0475e4175855
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
yqiancolumbia
parents:
diff
changeset
|
5 </command> |
0475e4175855
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
yqiancolumbia
parents:
diff
changeset
|
6 |
0475e4175855
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
yqiancolumbia
parents:
diff
changeset
|
7 <inputs> |
0475e4175855
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
yqiancolumbia
parents:
diff
changeset
|
8 <param name="input" type="data" format="bed" label="Input BED file in which CLIP tags with deletions were removed"/> |
0475e4175855
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
yqiancolumbia
parents:
diff
changeset
|
9 <param name="NeighborRegion" type="text" value="up" label="Get neighbor region relative to up|down|r=100"/> |
0475e4175855
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
yqiancolumbia
parents:
diff
changeset
|
10 <param name="LeftExtension" type="integer" value="-1" label="Extension on the left, with sign 0"/> |
0475e4175855
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
yqiancolumbia
parents:
diff
changeset
|
11 <param name="RightExtension" type="integer" value="-1" label="Extension on the right, with sign 0"/> |
0475e4175855
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
yqiancolumbia
parents:
diff
changeset
|
12 </inputs> |
0475e4175855
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
yqiancolumbia
parents:
diff
changeset
|
13 |
0475e4175855
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
yqiancolumbia
parents:
diff
changeset
|
14 <outputs> |
0475e4175855
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
yqiancolumbia
parents:
diff
changeset
|
15 <data name="output" format="bed" label="Output file in BED format extended around start site as a potential cross link site that causes truncation" /> |
0475e4175855
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
yqiancolumbia
parents:
diff
changeset
|
16 </outputs> |
0475e4175855
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
yqiancolumbia
parents:
diff
changeset
|
17 <help> |
0475e4175855
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
yqiancolumbia
parents:
diff
changeset
|
18 |
0475e4175855
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
yqiancolumbia
parents:
diff
changeset
|
19 .. class:: infomark |
0475e4175855
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
yqiancolumbia
parents:
diff
changeset
|
20 |
0475e4175855
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
yqiancolumbia
parents:
diff
changeset
|
21 **What this tool does** |
0475e4175855
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
yqiancolumbia
parents:
diff
changeset
|
22 |
0475e4175855
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
yqiancolumbia
parents:
diff
changeset
|
23 This tool will extract sequences specied by a bed file. |
0475e4175855
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
yqiancolumbia
parents:
diff
changeset
|
24 |
0475e4175855
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
yqiancolumbia
parents:
diff
changeset
|
25 Here it will take as input files in BED format in which CLIP tags with deletions were removed and output files in BED format extended around start site as a potential cross link site that causes truncation. |
0475e4175855
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
yqiancolumbia
parents:
diff
changeset
|
26 </help> |
0475e4175855
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
yqiancolumbia
parents:
diff
changeset
|
27 </tool> |
0475e4175855
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
yqiancolumbia
parents:
diff
changeset
|
28 |