Mercurial > repos > iuc > seqtk
annotate seqtk_mergepe.xml @ 7:55e75a28fde7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 344140b8df53b8b7024618bb04594607a045c03a
| author | iuc |
|---|---|
| date | Mon, 04 May 2015 22:47:23 -0400 |
| parents | 33ded39275c3 |
| children | 16f2535c08bf |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 2 <tool id="seqtk_mergepe" name="seqtk_mergepe" version="@WRAPPER_VERSION@.0"> | |
| 3 <description>interleave two unpaired FASTA/Q files for a paired-end file</description> | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements"/> | |
| 8 <expand macro="stdio"/> | |
| 9 <command><![CDATA[seqtk mergepe | |
| 10 $in_fq1 | |
| 11 $in_fq2 | |
| 12 > $default]]></command> | |
| 13 <inputs> | |
| 14 <param name="in_fq1" type="data" format="fasta,fastq" label="Input FASTA/Q file #1"/> | |
| 15 <param name="in_fq2" type="data" format="fasta,fastq" label="Input FASTA/Q file #2"/> | |
| 16 </inputs> | |
| 17 <outputs> | |
| 18 <data format_source="in_fq1" hidden="false" name="default" label="$in_fq1.name and $in_fq2.name as interleaved paired-end"/> | |
| 19 </outputs> | |
| 20 <tests> | |
| 21 <test> | |
| 22 <param name="in_fq1" value="paired_dat1.fq"/> | |
| 23 <param name="in_fq2" value="paired_dat2.fq"/> | |
| 24 <output name="default" file="paired_dat.fq" ftype="fastq"/> | |
| 25 </test> | |
| 26 </tests> | |
| 27 <help><![CDATA[ | |
| 28 **What it does** | |
| 29 | |
| 30 Merge two files which constitute a paired-end file into a single, interleaved, paired-end FASTA/Q file | |
| 31 | |
| 32 :: | |
| 33 | |
| 34 # r1.fq | |
| 35 @test-6/1 | |
| 36 AGCTTGACGC | |
| 37 + | |
| 38 ?.HCF@C>>F | |
| 39 | |
| 40 # r2.fq | |
| 41 @test-6/2 | |
| 42 TGCGAAGACC | |
| 43 + | |
| 44 >2?A?A@@7? | |
| 45 | |
| 46 will produce the following paired file: | |
| 47 | |
| 48 :: | |
| 49 | |
| 50 @test-6/1 | |
| 51 AGCTTGACGC | |
| 52 + | |
| 53 ?.HCF@C>>F | |
| 54 @test-6/2 | |
| 55 TGCGAAGACC | |
| 56 + | |
| 57 >2?A?A@@7? | |
| 58 | |
| 59 While this may not have been an illuminating example, it is important to note | |
| 60 that this tool will properly interleave data. For example if you have the ids: | |
| 61 | |
| 62 :: | |
| 63 | |
| 64 @r-1/1 | |
| 65 @r-2/1 | |
| 66 @r-3/1 | |
| 67 @r-4/1 | |
| 68 | |
| 69 and | |
| 70 | |
| 71 :: | |
| 72 | |
| 73 @r-1/2 | |
| 74 @r-2/2 | |
| 75 @r-3/2 | |
| 76 @r-4/2 | |
| 77 | |
| 78 These will be interleaved as | |
| 79 | |
| 80 :: | |
| 81 | |
| 82 @r-1/1 | |
| 83 @r-1/2 | |
| 84 @r-2/1 | |
| 85 @r-2/2 | |
| 86 @r-3/1 | |
| 87 @r-3/2 | |
| 88 @r-4/1 | |
| 89 @r-4/2 | |
| 90 | |
| 91 @ATTRIBUTION@ | |
| 92 ]]></help> | |
|
7
55e75a28fde7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
0
diff
changeset
|
93 <expand macro="citation" /> |
| 0 | 94 </tool> |