Mercurial > repos > iuc > seqtk

annotate seqtk_fqchk.xml @ 9:4b494533146a 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 2f75805e2e6cfa2af15076e6f4929b87631360a6
author iuc
date Sat, 09 Dec 2023 11:14:21 +0000
parents 3da72230c066
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
9
4b494533146a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 2f75805e2e6cfa2af15076e6f4929b87631360a6
iuc
parents: 8
diff changeset
2 <tool id="seqtk_fqchk" name="seqtk_fqchk" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
3
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
3 <description>fastq QC (base/quality summary)</description>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
4 <macros>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
5 <import>macros.xml</import>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
6 </macros>
9
4b494533146a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 2f75805e2e6cfa2af15076e6f4929b87631360a6
iuc
parents: 8
diff changeset
7 <expand macro="bio_tools"/>
5
a09586d5149a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 83ecfe7d9bbf03c91f27ba18776352a1ebf8cf6f
iuc
parents: 4
diff changeset
8 <expand macro="requirements">
a09586d5149a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 83ecfe7d9bbf03c91f27ba18776352a1ebf8cf6f
iuc
parents: 4
diff changeset
9 <requirement type="package" version="@AWK_VERSION@">gawk</requirement>
a09586d5149a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 83ecfe7d9bbf03c91f27ba18776352a1ebf8cf6f
iuc
parents: 4
diff changeset
10 </expand>
3
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
11 <expand macro="stdio"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
12 <command><![CDATA[
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
13 seqtk fqchk
0
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
14 -q $q
3
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
15 '$in_file' | awk '{if(NR<4){print "#"$0}else{print $0}}'
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
16 > '$default'
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
17 ]]></command>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
18 <inputs>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
19 <expand macro="in_fq"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
20 <param argument="-q" type="integer" value="20" label="Quality values" help="Use 0 to get the distribution of all quality values"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
21 </inputs>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
22 <outputs>
9
4b494533146a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 2f75805e2e6cfa2af15076e6f4929b87631360a6
iuc
parents: 8
diff changeset
23 <data name="default" format="tabular" label="${tool.name} on ${on_string}: Quality information"/>
3
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
24 </outputs>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
25 <tests>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
26 <test>
4
ecf1c30da3a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 3
diff changeset
27 <param name="in_file" value="seqtk_fqchk.fq" ftype="fastq"/>
ecf1c30da3a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 3
diff changeset
28 <output name="default" file="seqtk_fqchk.out" ftype="tabular"/>
ecf1c30da3a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 3
diff changeset
29 </test>
ecf1c30da3a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 3
diff changeset
30 <test>
ecf1c30da3a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 3
diff changeset
31 <param name="in_file" value="seqtk_fqchk.fq.gz" ftype="fastq.gz"/>
3
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
32 <output name="default" file="seqtk_fqchk.out" ftype="tabular"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
33 </test>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
34 </tests>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
35 <help><![CDATA[
0
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
36 **What it does**
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
37
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
38 Returns quality score information base-by-base.
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
39
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
40 ::
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
41
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
42 @SEQ_ID1
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
43 GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
44 +
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
45 !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
46
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
47 each based is examined individually and information reported:
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
48
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
49 ::
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
50
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
51 #min_len: 60; max_len: 60; avg_len: 60.00; 15 distinct quality values
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
52 #POS #bases %A %C %G %T %N avgQ errQ %low %high
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
53 #ALL 60 31.7 16.7 18.3 33.3 0.0 15.1 8.7 66.7 33.3
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
54 1 1 0.0 0.0 100.0 0.0 0.0 0.0 3.0 100.0 0.0
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
55 2 1 100.0 0.0 0.0 0.0 0.0 6.0 6.0 100.0 0.0
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
56 3 1 0.0 0.0 0.0 100.0 0.0 6.0 6.0 100.0 0.0
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
57 4 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
58 5 1 0.0 0.0 0.0 100.0 0.0 7.0 7.0 100.0 0.0
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
59 6 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
60 7 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
61 8 1 0.0 0.0 100.0 0.0 0.0 7.0 7.0 100.0 0.0
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
62 9 1 0.0 0.0 100.0 0.0 0.0 9.0 9.0 100.0 0.0
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
63 10 1 0.0 0.0 0.0 100.0 0.0 9.0 9.0 100.0 0.0
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
64
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
65 @ATTRIBUTION@
3
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
66 ]]></help>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 2
diff changeset
67 <expand macro="citation" />
0
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
68 </tool>