Mercurial > repos > jjohnson > fgbio_sort_bam

comparison macros.xml @ 0:286e35cf3f1c draft

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"planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
author jjohnson
date Sun, 21 Feb 2021 23:41:16 +0000
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-1:000000000000 0:286e35cf3f1c
1 <macros>
2 <token name="@TOOL_VERSION@">1.3.0</token>
3 <token name="@VERSION_SUFFIX@">0</token>
4 <xml name="requirements">
5 <requirements>
6 <requirement type="package" version="@TOOL_VERSION@">fgbio</requirement>
7 <yield/>
8 </requirements>
9 </xml>
10 <token name="@READ_STRUCTURE_PATTERN@">(([1-9][0-9]*[TBMS])*([+]|[1-9][0-9]*)[TBMS])</token>
11 <token name="@READ_STRUCTURES_PATTERN@">@READ_STRUCTURE_PATTERN@(\s@READ_STRUCTURE_PATTERN@)*</token>
12 <xml name="read_structures_validator">
13 <validator type="regex" message="">^@READ_STRUCTURES_PATTERN@$</validator>
14 </xml>
15 <xml name="sam_tag_validator">
16 <validator type="regex" message="">^[A-Za-z][A-Za-z]$</validator>
17 </xml>
18 <xml name="sam_sort_order">
19 <param argument="--sort-order" type="select" optional="true" label="Sort BAM by">
20 <option value="Coordinate">Coordinate</option>
21 <option value="Queryname">Queryname</option>
22 <option value="Random">Random</option>
23 <option value="RandomQuery">RandomQuery</option>
24 </param>
25 </xml>
26
27 <token name="@READ_STRUCTURES_HELP@"><![CDATA[
28 **Read Structures**
29
30 Read structures are made up of <number><operator> pairs much like the CIGAR string in BAM files. Four kinds of operators are recognized:
31
32 T identifies a template read
33 B identifies a sample barcode read
34 M identifies a unique molecular index read
35 S identifies a set of bases that should be skipped or ignored
36
37 The last <number><operator> pair may be specified using a + sign instead of number to denote “all remaining bases”. This is useful if, e.g., fastqs have been trimmed and contain reads of varying length. For example to convert a paired-end run with an index read and where the first 5 bases of R1 are a UMI and the second five bases are monotemplate you might specify:
38
39 ::
40
41 --input r1.fq r2.fq i1.fq --read-structures 5M5S+T +T +B
42
43 Alternative if you know your reads are of fixed length you could specify:
44
45 ::
46
47 --input r1.fq r2.fq i1.fq --read-structures 5M5S65T 75T 8B
48
49
50 ]]></token>
51 <xml name="citations">
52 <citations>
53 <yield />
54 </citations>
55 </xml>
56 </macros>