Mercurial > repos > iuc > seqtk

annotate seqtk_fqchk.xml @ 2:f73729b62b51 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 2249d643284ee782d882cd200729a86a2c6bb744
author iuc
date Fri, 01 Jan 2016 14:49:42 -0500
parents e0a0fd938de4
children bc7d99f46a5d
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"?>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
2 <tool id="seqtk_fqchk" name="seqtk_fqchk" version="@WRAPPER_VERSION@.0">
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
3 <description>fastq QC (base/quality summary)</description>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
4 <macros>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
5 <import>macros.xml</import>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
6 </macros>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
7 <expand macro="requirements"/>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
8 <expand macro="stdio"/>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
9 <command><![CDATA[seqtk fqchk
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
10 -q $q
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
11 $in_file | awk '{if(NR<4){print "#"$0}else{print $0}}'
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
12 > $default]]></command>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
13 <inputs>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
14 <expand macro="in_fq"/>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
15 <param name="q" type="integer" value="20" label="quality values" help="use 0 to get the distribution of all quality values (-q)"/>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
16 </inputs>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
17 <outputs>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
18 <data format="tabular" hidden="false" name="default" label="Quality information for $in_file.name"/>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
19 </outputs>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
20 <tests>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
21 <test>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
22 <param name="in_file" value="seqtk_fqchk.fq"/>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
23 <output name="default" file="seqtk_fqchk.out" ftype="tabular"/>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
24 </test>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
25 </tests>
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
26 <help><![CDATA[
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
27 **What it does**
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
28
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
29 Returns quality score information base-by-base.
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
30
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
31 ::
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
32
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
33 @SEQ_ID1
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
34 GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
35 +
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
36 !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
37
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
38 each based is examined individually and information reported:
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 #min_len: 60; max_len: 60; avg_len: 60.00; 15 distinct quality values
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
43 #POS #bases %A %C %G %T %N avgQ errQ %low %high
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
44 #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
45 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
46 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
47 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
48 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
49 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
50 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
51 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
52 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
53 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
54 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
55
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
56 @ATTRIBUTION@
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
57 ]]></help>
2
f73729b62b51 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 2249d643284ee782d882cd200729a86a2c6bb744
iuc
parents: 0
diff changeset
58 <expand macro="citation" />
0
e0a0fd938de4 Uploaded
iuc
parents:
diff changeset
59 </tool>