Mercurial > repos > yqiancolumbia > ctk_test
comparison removeRow.xml @ 0:0475e4175855 draft default tip
planemo upload commit 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071-dirty
author | yqiancolumbia |
---|---|
date | Mon, 30 Apr 2018 05:25:11 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:0475e4175855 |
---|---|
1 <tool id="removeRow" name="Remove CLIP tags with deletions"> | |
2 <description></description> | |
3 | |
4 <command interpreter="perl"> | |
5 /home/galaxy/tools/CTK/removeRow.pl -q $QueryColumnID -f $FilterColumnID $IgnoreCase $ReverseMode $input1 $input2 > $output | |
6 </command> | |
7 | |
8 <inputs> | |
9 <param type="data" format="bed" name="input1" label="Input file in BED format of unique CLIP tags"/> | |
10 <param type="data" format="bed" name="input2" label="Input file in BED format of CIMS" /> | |
11 | |
12 <param name="QueryColumnID" type="integer" value="3" label="Query column id (zero-based)"/> | |
13 <param name="FilterColumnID" type="integer" value="3" label="Filter column id (zero-based)"/> | |
14 | |
15 <param name="IgnoreCase" type="boolean" truevalue="-i" falsevalue="" checked="no" label="Ignore case" /> | |
16 <param name="ReverseMode" type="boolean" truevalue="-r" falsevalue="" checked="no" label="Reverse mode" /> | |
17 </inputs> | |
18 | |
19 <outputs> | |
20 <data name="output" format="bed" /> | |
21 </outputs> | |
22 <help> | |
23 | |
24 .. class:: infomark | |
25 | |
26 **What this tool does** | |
27 | |
28 Since the vast majority of deletions are introduced because of cross linking, tags with deletions are treated as read-through tags and removed. | |
29 | |
30 This tool will remove selected rows from a file. Here it will output file in BED format in which CLIP tags with deletions are removed. | |
31 | |
32 Note: The parameters 3 and 3 indicate the columns in the two input files. | |
33 </help> | |
34 </tool> |