comparison seqtk_fqchk.xml @ 0:e0a0fd938de4 draft

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author iuc
date Thu, 05 Feb 2015 11:52:40 -0500
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-1:000000000000 0:e0a0fd938de4
1 <?xml version="1.0"?>
2 <tool id="seqtk_fqchk" name="seqtk_fqchk" version="@WRAPPER_VERSION@.0">
3 <description>fastq QC (base/quality summary)</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <expand macro="stdio"/>
9 <command><![CDATA[seqtk fqchk
10 -q $q
11 $in_file | awk '{if(NR<4){print "#"$0}else{print $0}}'
12 > $default]]></command>
13 <inputs>
14 <expand macro="in_fq"/>
15 <param name="q" type="integer" value="20" label="quality values" help="use 0 to get the distribution of all quality values (-q)"/>
16 </inputs>
17 <outputs>
18 <data format="tabular" hidden="false" name="default" label="Quality information for $in_file.name"/>
19 </outputs>
20 <tests>
21 <test>
22 <param name="in_file" value="seqtk_fqchk.fq"/>
23 <output name="default" file="seqtk_fqchk.out" ftype="tabular"/>
24 </test>
25 </tests>
26 <help><![CDATA[
27 **What it does**
28
29 Returns quality score information base-by-base.
30
31 ::
32
33 @SEQ_ID1
34 GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
35 +
36 !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65
37
38 each based is examined individually and information reported:
39
40 ::
41
42 #min_len: 60; max_len: 60; avg_len: 60.00; 15 distinct quality values
43 #POS #bases %A %C %G %T %N avgQ errQ %low %high
44 #ALL 60 31.7 16.7 18.3 33.3 0.0 15.1 8.7 66.7 33.3
45 1 1 0.0 0.0 100.0 0.0 0.0 0.0 3.0 100.0 0.0
46 2 1 100.0 0.0 0.0 0.0 0.0 6.0 6.0 100.0 0.0
47 3 1 0.0 0.0 0.0 100.0 0.0 6.0 6.0 100.0 0.0
48 4 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0
49 5 1 0.0 0.0 0.0 100.0 0.0 7.0 7.0 100.0 0.0
50 6 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0
51 7 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0
52 8 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0
53 9 1 0.0 0.0 100.0 0.0 0.0 9.0 9.0 100.0 0.0
54 10 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0
55
56 @ATTRIBUTION@
57 ]]></help>
58 </tool>