Mercurial > repos > jjohnson > fgbio_call_molecular_consensus_reads

annotate macros.xml @ 0:0ad5327b80cc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
author jjohnson
date Sun, 21 Feb 2021 23:40:53 +0000
parents
children b7795c2f0b81
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
1 <macros>
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
2 <token name="@TOOL_VERSION@">1.3.0</token>
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
3 <token name="@VERSION_SUFFIX@">0</token>
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
4 <xml name="requirements">
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
5 <requirements>
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
6 <requirement type="package" version="@TOOL_VERSION@">fgbio</requirement>
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
7 <yield/>
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
8 </requirements>
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
9 </xml>
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
10 <token name="@READ_STRUCTURE_PATTERN@">(([1-9][0-9]*[TBMS])*([+]|[1-9][0-9]*)[TBMS])</token>
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
11 <token name="@READ_STRUCTURES_PATTERN@">@READ_STRUCTURE_PATTERN@(\s@READ_STRUCTURE_PATTERN@)*</token>
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
12 <xml name="read_structures_validator">
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
13 <validator type="regex" message="">^@READ_STRUCTURES_PATTERN@$</validator>
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
14 </xml>
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
15 <xml name="sam_tag_validator">
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
16 <validator type="regex" message="">^[A-Za-z][A-Za-z]$</validator>
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
17 </xml>
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
18 <xml name="sam_sort_order">
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
19 <param argument="--sort-order" type="select" optional="true" label="Sort BAM by">
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
20 <option value="Coordinate">Coordinate</option>
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
21 <option value="Queryname">Queryname</option>
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
22 <option value="Random">Random</option>
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
23 <option value="RandomQuery">RandomQuery</option>
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
24 </param>
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
25 </xml>
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
26
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
27 <token name="@READ_STRUCTURES_HELP@"><![CDATA[
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
28 **Read Structures**
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
29
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
30 Read structures are made up of <number><operator> pairs much like the CIGAR string in BAM files. Four kinds of operators are recognized:
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
31
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
32 T identifies a template read
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
33 B identifies a sample barcode read
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
34 M identifies a unique molecular index read
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
35 S identifies a set of bases that should be skipped or ignored
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
36
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
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:
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
38
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
39 ::
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
40
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
41 --input r1.fq r2.fq i1.fq --read-structures 5M5S+T +T +B
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
42
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
43 Alternative if you know your reads are of fixed length you could specify:
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
44
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
45 ::
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
46
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
47 --input r1.fq r2.fq i1.fq --read-structures 5M5S65T 75T 8B
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
48
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
49
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
50 ]]></token>
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
51 <xml name="citations">
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
52 <citations>
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
53 <yield />
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
54 </citations>
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
55 </xml>
0ad5327b80cc "planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
jjohnson
parents:
diff changeset
56 </macros>