Mercurial > repos > jjohnson > fgbio_sort_bam
comparison macros.xml @ 1:cb58d1961fd3 draft
"planemo upload commit 692ea558cbbefee93859dc2b005fab5ac4970eb8"
author | jjohnson |
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date | Wed, 24 Feb 2021 13:02:43 +0000 |
parents | 286e35cf3f1c |
children | f8798f04ac47 |
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0:286e35cf3f1c | 1:cb58d1961fd3 |
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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 |