Mercurial > repos > iuc > seqtk

comparison seqtk_comp.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_comp" name="seqtk_comp" version="@WRAPPER_VERSION@.0">
3 <description>get the nucleotide composition of FASTA/Q</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <expand macro="stdio"/>
9 <command><![CDATA[seqtk comp
10 #if $in_bed:
11 -r $in_bed
12 #end if
13
14 $in_file | awk 'BEGIN{print "#chr\tlength\t#A\t#C\t#G\t#T\t#2\t#3\t#4\t#CpG\t#tv\t#ts\t#CpG-ts"}1'
15
16 > $default]]></command>
17 <inputs>
18 <expand macro="in_faq"/>
19 <param name="in_bed" optional="True" type="data" format="bed" label="bed file"/>
20 </inputs>
21 <outputs>
22 <data format="tabular" hidden="false" name="default" label="Nucleotide composition of $in_file.name"/>
23 </outputs>
24 <tests>
25 <test>
26 <param name="in_file" value="seqtk_comp.fa" ftype="fasta"/>
27 <output name="default" file="seqtk_comp.out" ftype="tabular"/>
28 </test>
29 </tests>
30 <help><![CDATA[
31 **What it does**
32
33 Reports composition of fasta/fastq sequences. For an example sequence like
34
35 ::
36 >test0
37 ACTGACTGAA
38 >ambig_ref
39 ACGTCGTGTTVHDBN
40
41 The seqtk tool will report:
42
43 ::
44
45 #chr length #A #C #G #T #2 #3 #4 #CpG #tv #ts #CpG-ts
46 test0 11 4 2 2 2 0 0 1 0 0 0 0
47 ambig_ref 15 1 2 3 4 0 4 1 4 0 0 0
48
49
50 @ATTRIBUTION@
51 ]]></help>
52 </tool>