Mercurial > repos > iuc > seqtk

comparison seqtk_cutN.xml @ 6:113f3c3d6bee draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author iuc
date Wed, 29 Apr 2015 22:47:00 -0400
parents 33ded39275c3
children 55e75a28fde7
comparison
equal deleted inserted replaced
5:fd11d2328ca8 6:113f3c3d6bee
1 <?xml version="1.0"?>
2 <tool id="seqtk_cutN" name="seqtk_cutN" version="@WRAPPER_VERSION@.0">
3 <description>cut sequence at long N</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <expand macro="stdio"/>
9 <command><![CDATA[seqtk cutN -n $n
10 -p $p
11 $g
12 $in_file
13 > $default]]></command>
14 <inputs>
15 <expand macro="in_faq"/>
16 <param label="min size of N tract" help="(-n)" name="n" type="integer" value="1000"/>
17 <param label="penalty for a non-N" help="(-p)" name="p" type="integer" value="10"/>
18 <param checked="false" label="print gaps only, no sequence" help="(-g)" name="g" type="boolean" falsevalue="" truevalue="-g"/>
19 </inputs>
20 <outputs>
21 <data format_source="in_file" hidden="false" name="default" label="$in_file.name split on N runs longer than $n"/>
22 </outputs>
23 <tests>
24 <test>
25 <param name="in_file" value="seqtk_cutn.fa"/>
26 <param name="n" value="1"/>
27 <output name="default" file="seqtk_cutn.out" ftype="fasta"/>
28 </test>
29 </tests>
30 <help><![CDATA[
31 **What it does**
32
33 Splits long sequences with runs of Ns
34
35 ::
36
37 >test
38 AACTGATCGATCGATCGNNNNNNNNNNNACATG
39
40 This will be split into the component sequences without the ambiguity.
41
42 ::
43
44 >test:1-17
45 AACTGATCGATCGATCG
46 >test:29-33
47 ACATG
48
49
50 @ATTRIBUTION@
51 ]]></help>
52 </tool>