Mercurial > repos > iuc > seqtk

annotate seqtk_fqchk.xml @ 18:1d63dbcecb10 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 50a0bd6d783a69e7303363a31130134767493e66"
author iuc
date Fri, 06 Sep 2019 09:09:35 -0400
parents 069c8f0695ee
children 8f26884c60b6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
17
069c8f0695ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 83ecfe7d9bbf03c91f27ba18776352a1ebf8cf6f
iuc
parents: 16
diff changeset
2 <tool id="seqtk_fqchk" name="seqtk_fqchk" version="@TOOL_VERSION@.1">
15
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
3 <description>fastq QC (base/quality summary)</description>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
4 <macros>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
5 <import>macros.xml</import>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
6 </macros>
17
069c8f0695ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 83ecfe7d9bbf03c91f27ba18776352a1ebf8cf6f
iuc
parents: 16
diff changeset
7 <expand macro="requirements">
069c8f0695ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 83ecfe7d9bbf03c91f27ba18776352a1ebf8cf6f
iuc
parents: 16
diff changeset
8 <requirement type="package" version="@AWK_VERSION@">gawk</requirement>
069c8f0695ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 83ecfe7d9bbf03c91f27ba18776352a1ebf8cf6f
iuc
parents: 16
diff changeset
9 </expand>
15
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
10 <expand macro="stdio"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
11 <command><![CDATA[
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
12 seqtk fqchk
0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
13 -q $q
15
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
14 '$in_file' | awk '{if(NR<4){print "#"$0}else{print $0}}'
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
15 > '$default'
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
16 ]]></command>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
17 <inputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
18 <expand macro="in_fq"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
19 <param argument="-q" type="integer" value="20" label="Quality values" help="Use 0 to get the distribution of all quality values"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
20 </inputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
21 <outputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
22 <data name="default" format="tabular" label="Quality information for $in_file.name"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
23 </outputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
24 <tests>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
25 <test>
16
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
26 <param name="in_file" value="seqtk_fqchk.fq" ftype="fastq"/>
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
27 <output name="default" file="seqtk_fqchk.out" ftype="tabular"/>
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
28 </test>
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
29 <test>
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
30 <param name="in_file" value="seqtk_fqchk.fq.gz" ftype="fastq.gz"/>
15
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
31 <output name="default" file="seqtk_fqchk.out" ftype="tabular"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
32 </test>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
33 </tests>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
34 <help><![CDATA[
0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
35 **What it does**
33ded39275c3 Uploaded
iuc
parents:
diff changeset
36
33ded39275c3 Uploaded
iuc
parents:
diff changeset
37 Returns quality score information base-by-base.
33ded39275c3 Uploaded
iuc
parents:
diff changeset
38
33ded39275c3 Uploaded
iuc
parents:
diff changeset
39 ::
33ded39275c3 Uploaded
iuc
parents:
diff changeset
40
33ded39275c3 Uploaded
iuc
parents:
diff changeset
41 @SEQ_ID1
33ded39275c3 Uploaded
iuc
parents:
diff changeset
42 GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
33ded39275c3 Uploaded
iuc
parents:
diff changeset
43 +
33ded39275c3 Uploaded
iuc
parents:
diff changeset
44 !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65
33ded39275c3 Uploaded
iuc
parents:
diff changeset
45
33ded39275c3 Uploaded
iuc
parents:
diff changeset
46 each based is examined individually and information reported:
33ded39275c3 Uploaded
iuc
parents:
diff changeset
47
33ded39275c3 Uploaded
iuc
parents:
diff changeset
48 ::
33ded39275c3 Uploaded
iuc
parents:
diff changeset
49
33ded39275c3 Uploaded
iuc
parents:
diff changeset
50 #min_len: 60; max_len: 60; avg_len: 60.00; 15 distinct quality values
33ded39275c3 Uploaded
iuc
parents:
diff changeset
51 #POS #bases %A %C %G %T %N avgQ errQ %low %high
33ded39275c3 Uploaded
iuc
parents:
diff changeset
52 #ALL 60 31.7 16.7 18.3 33.3 0.0 15.1 8.7 66.7 33.3
33ded39275c3 Uploaded
iuc
parents:
diff changeset
53 1 1 0.0 0.0 100.0 0.0 0.0 0.0 3.0 100.0 0.0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
54 2 1 100.0 0.0 0.0 0.0 0.0 6.0 6.0 100.0 0.0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
55 3 1 0.0 0.0 0.0 100.0 0.0 6.0 6.0 100.0 0.0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
56 4 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
57 5 1 0.0 0.0 0.0 100.0 0.0 7.0 7.0 100.0 0.0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
58 6 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
59 7 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
60 8 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
61 9 1 0.0 0.0 100.0 0.0 0.0 9.0 9.0 100.0 0.0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
62 10 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
63
33ded39275c3 Uploaded
iuc
parents:
diff changeset
64 @ATTRIBUTION@
15
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
65 ]]></help>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
66 <expand macro="citation" />
0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
67 </tool>