Mercurial > repos > iuc > seqtk

annotate seqtk_mergepe.xml @ 16:48a51c72f5e7 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 ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
author iuc
date Wed, 17 Oct 2018 05:58:58 -0400
parents 16f2535c08bf
children 069c8f0695ee
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"?>
33ded39275c3 Uploaded
iuc
parents:
diff changeset
2 <tool id="seqtk_mergepe" name="seqtk_mergepe" version="@WRAPPER_VERSION@.0">
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>interleave two unpaired FASTA/Q files for a paired-end file</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>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
7 <expand macro="requirements"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
8 <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
9 <command><![CDATA[
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
10 seqtk mergepe
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
11 '$in_fq1'
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
12 '$in_fq2'
16
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
13 #echo "| gzip --no-name" if $in_fq1.is_of_type('fasta.gz', 'fastq.gz') else "" # > '$default'
15
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
14 ]]></command>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
15 <inputs>
16
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
16 <param name="in_fq1" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #1"/>
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
17 <param name="in_fq2" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #2"/>
15
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
18 </inputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
19 <outputs>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
20 <data name="default" format_source="in_fq1" label="$in_fq1.name and $in_fq2.name as interleaved paired-end"/>
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 <tests>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
23 <test>
16
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
24 <param name="in_fq1" value="paired_dat1.fq" ftype="fastqsanger"/>
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
25 <param name="in_fq2" value="paired_dat2.fq" ftype="fastqsanger"/>
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
26 <output name="default" file="paired_dat.fq" ftype="fastqsanger"/>
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
27 </test>
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 <param name="in_fq1" value="paired_dat1.fq.gz" ftype="fastqsanger.gz"/>
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_fq2" value="paired_dat2.fq.gz" ftype="fastqsanger.gz"/>
48a51c72f5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
iuc
parents: 15
diff changeset
31 <output name="default" file="paired_dat.fq.gz" ftype="fastqsanger.gz"/>
15
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 Merge two files which constitute a paired-end file into a single, interleaved, paired-end FASTA/Q file
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 # r1.fq
33ded39275c3 Uploaded
iuc
parents:
diff changeset
42 @test-6/1
33ded39275c3 Uploaded
iuc
parents:
diff changeset
43 AGCTTGACGC
33ded39275c3 Uploaded
iuc
parents:
diff changeset
44 +
33ded39275c3 Uploaded
iuc
parents:
diff changeset
45 ?.HCF@C>>F
33ded39275c3 Uploaded
iuc
parents:
diff changeset
46
33ded39275c3 Uploaded
iuc
parents:
diff changeset
47 # r2.fq
33ded39275c3 Uploaded
iuc
parents:
diff changeset
48 @test-6/2
33ded39275c3 Uploaded
iuc
parents:
diff changeset
49 TGCGAAGACC
33ded39275c3 Uploaded
iuc
parents:
diff changeset
50 +
33ded39275c3 Uploaded
iuc
parents:
diff changeset
51 >2?A?A@@7?
33ded39275c3 Uploaded
iuc
parents:
diff changeset
52
33ded39275c3 Uploaded
iuc
parents:
diff changeset
53 will produce the following paired file:
33ded39275c3 Uploaded
iuc
parents:
diff changeset
54
33ded39275c3 Uploaded
iuc
parents:
diff changeset
55 ::
33ded39275c3 Uploaded
iuc
parents:
diff changeset
56
33ded39275c3 Uploaded
iuc
parents:
diff changeset
57 @test-6/1
33ded39275c3 Uploaded
iuc
parents:
diff changeset
58 AGCTTGACGC
33ded39275c3 Uploaded
iuc
parents:
diff changeset
59 +
33ded39275c3 Uploaded
iuc
parents:
diff changeset
60 ?.HCF@C>>F
33ded39275c3 Uploaded
iuc
parents:
diff changeset
61 @test-6/2
33ded39275c3 Uploaded
iuc
parents:
diff changeset
62 TGCGAAGACC
33ded39275c3 Uploaded
iuc
parents:
diff changeset
63 +
33ded39275c3 Uploaded
iuc
parents:
diff changeset
64 >2?A?A@@7?
33ded39275c3 Uploaded
iuc
parents:
diff changeset
65
33ded39275c3 Uploaded
iuc
parents:
diff changeset
66 While this may not have been an illuminating example, it is important to note
33ded39275c3 Uploaded
iuc
parents:
diff changeset
67 that this tool will properly interleave data. For example if you have the ids:
33ded39275c3 Uploaded
iuc
parents:
diff changeset
68
33ded39275c3 Uploaded
iuc
parents:
diff changeset
69 ::
33ded39275c3 Uploaded
iuc
parents:
diff changeset
70
33ded39275c3 Uploaded
iuc
parents:
diff changeset
71 @r-1/1
33ded39275c3 Uploaded
iuc
parents:
diff changeset
72 @r-2/1
33ded39275c3 Uploaded
iuc
parents:
diff changeset
73 @r-3/1
33ded39275c3 Uploaded
iuc
parents:
diff changeset
74 @r-4/1
33ded39275c3 Uploaded
iuc
parents:
diff changeset
75
33ded39275c3 Uploaded
iuc
parents:
diff changeset
76 and
33ded39275c3 Uploaded
iuc
parents:
diff changeset
77
33ded39275c3 Uploaded
iuc
parents:
diff changeset
78 ::
33ded39275c3 Uploaded
iuc
parents:
diff changeset
79
33ded39275c3 Uploaded
iuc
parents:
diff changeset
80 @r-1/2
33ded39275c3 Uploaded
iuc
parents:
diff changeset
81 @r-2/2
33ded39275c3 Uploaded
iuc
parents:
diff changeset
82 @r-3/2
33ded39275c3 Uploaded
iuc
parents:
diff changeset
83 @r-4/2
33ded39275c3 Uploaded
iuc
parents:
diff changeset
84
33ded39275c3 Uploaded
iuc
parents:
diff changeset
85 These will be interleaved as
33ded39275c3 Uploaded
iuc
parents:
diff changeset
86
33ded39275c3 Uploaded
iuc
parents:
diff changeset
87 ::
33ded39275c3 Uploaded
iuc
parents:
diff changeset
88
33ded39275c3 Uploaded
iuc
parents:
diff changeset
89 @r-1/1
33ded39275c3 Uploaded
iuc
parents:
diff changeset
90 @r-1/2
33ded39275c3 Uploaded
iuc
parents:
diff changeset
91 @r-2/1
33ded39275c3 Uploaded
iuc
parents:
diff changeset
92 @r-2/2
33ded39275c3 Uploaded
iuc
parents:
diff changeset
93 @r-3/1
33ded39275c3 Uploaded
iuc
parents:
diff changeset
94 @r-3/2
33ded39275c3 Uploaded
iuc
parents:
diff changeset
95 @r-4/1
33ded39275c3 Uploaded
iuc
parents:
diff changeset
96 @r-4/2
33ded39275c3 Uploaded
iuc
parents:
diff changeset
97
33ded39275c3 Uploaded
iuc
parents:
diff changeset
98 @ATTRIBUTION@
15
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
99 ]]></help>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
iuc
parents: 7
diff changeset
100 <expand macro="citation" />
0
33ded39275c3 Uploaded
iuc
parents:
diff changeset
101 </tool>