Mercurial > repos > jjohnson > fgbio_call_molecular_consensus_reads

comparison macros.xml @ 1:b7795c2f0b81 draft

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"planemo upload commit 692ea558cbbefee93859dc2b005fab5ac4970eb8"
author jjohnson
date Wed, 24 Feb 2021 13:02:26 +0000
parents 0ad5327b80cc
children d469e546604b
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0:0ad5327b80cc 1:b7795c2f0b81
15 <xml name="sam_tag_validator"> 15 <xml name="sam_tag_validator">
16 <validator type="regex" message="">^[A-Za-z][A-Za-z]$</validator> 16 <validator type="regex" message="">^[A-Za-z][A-Za-z]$</validator>
17 </xml> 17 </xml>
18 <xml name="sam_sort_order"> 18 <xml name="sam_sort_order">
19 <param argument="--sort-order" type="select" optional="true" label="Sort BAM by"> 19 <param argument="--sort-order" type="select" optional="true" label="Sort BAM by">
20 <option value="TemplateCoordinate">TemplateCoordinate</option>
20 <option value="Coordinate">Coordinate</option> 21 <option value="Coordinate">Coordinate</option>
21 <option value="Queryname">Queryname</option> 22 <option value="Queryname">Queryname</option>
22 <option value="Random">Random</option> 23 <option value="Random">Random</option>
23 <option value="RandomQuery">RandomQuery</option> 24 <option value="RandomQuery">RandomQuery</option>
24 </param> 25 </param>
26 </xml>
27
28 <xml name="sort_order_change_format">
29 <change_format>
30 <when input="sort_order" value="Coordinate" format="bam" />
31 <when input="sort_order" value="TemplateCoordinate" format="bam" />
32 <when input="sort_order" value="QueryName" format="unsorted.bam" />
33 <when input="sort_order" value="Random" format="unsorted.bam" />
34 <when input="sort_order" value="RandomQuery" format="unsorted.bam" />
35 </change_format>
25 </xml> 36 </xml>
26 37
27 <token name="@READ_STRUCTURES_HELP@"><![CDATA[ 38 <token name="@READ_STRUCTURES_HELP@"><![CDATA[
28 **Read Structures** 39 **Read Structures**
29 40
30 Read structures are made up of <number><operator> pairs much like the CIGAR string in BAM files. Four kinds of operators are recognized: 41 Read structures are made up of <number><operator> pairs much like the CIGAR string in BAM files. Four kinds of operators are recognized:
31 42
32 T identifies a template read 43 - T identifies a template read
33 B identifies a sample barcode read 44 - B identifies a sample barcode read
34 M identifies a unique molecular index read 45 - M identifies a unique molecular index read
35 S identifies a set of bases that should be skipped or ignored 46 - S identifies a set of bases that should be skipped or ignored
36 47
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: 48 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 49
39 :: 50 ::
40 51