Mercurial > repos > jjohnson > fgbio_group_reads_by_umi
comparison fgbio_group_reads_by_umi.xml @ 1:568816308859 draft
"planemo upload commit 692ea558cbbefee93859dc2b005fab5ac4970eb8"
| author | jjohnson |
|---|---|
| date | Wed, 24 Feb 2021 13:02:09 +0000 |
| parents | 900cd2865768 |
| children |
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| 0:900cd2865768 | 1:568816308859 |
|---|---|
| 49 otherwise discard reads with UMIs shorter than this length | 49 otherwise discard reads with UMIs shorter than this length |
| 50 and allow for differing UMI lengths. | 50 and allow for differing UMI lengths. |
| 51 </help> | 51 </help> |
| 52 </param> | 52 </param> |
| 53 <param argument="--min-map-q" type="integer" value="" optional="true" label="Minimum mapping quality" help="Default: 30"/> | 53 <param argument="--min-map-q" type="integer" value="" optional="true" label="Minimum mapping quality" help="Default: 30"/> |
| 54 <param argument="--raw-tag" type="text" value="" label="The tag containing the raw UMI" help="Default: RX"> | 54 <param argument="--raw-tag" type="text" value="" optional="true" label="The tag containing the raw UMI" help="Default: RX"> |
| 55 <expand macro="sam_tag_validator"/> | 55 <expand macro="sam_tag_validator"/> |
| 56 </param> | 56 </param> |
| 57 <param argument="--assign-tag" type="text" value="" label="The output tag for UMI grouping" help="Default: MI"> | 57 <param argument="--assign-tag" type="text" value="" optional="true" label="The output tag for UMI grouping" help="Default: MI"> |
| 58 <expand macro="sam_tag_validator"/> | 58 <expand macro="sam_tag_validator"/> |
| 59 </param> | 59 </param> |
| 60 <param argument="--include-non-pf-reads" type="select" value="true" optional="true" label="Include non-PF reads"> | 60 <param argument="--include-non-pf-reads" type="select" value="true" optional="true" label="Include non-PF reads"> |
| 61 <option value="true">Yes</option> | 61 <option value="true">Yes</option> |
| 62 <option value="flse">No</option> | 62 <option value="flse">No</option> |
| 66 | 66 |
| 67 </inputs> | 67 </inputs> |
| 68 <outputs> | 68 <outputs> |
| 69 <data name="family_size_histogram" format="tabular" > | 69 <data name="family_size_histogram" format="tabular" > |
| 70 <filter>output_counts == True</filter> | 70 <filter>output_counts == True</filter> |
| 71 <actions> | |
| 72 <action name="comment_lines" type="metadata" default="1" /> | |
| 73 <action name="column_names" type="metadata" default="family_size,count,fraction,fraction_gt_or_eq_family_size" /> | |
| 74 </actions> | |
| 71 </data> | 75 </data> |
| 72 <data name="output" format="bam" /> | 76 <data name="output" format="unsorted.bam" > |
| 77 <expand macro="sort_order_change_format" /> | |
| 78 </data> | |
| 73 </outputs> | 79 </outputs> |
| 74 <help><![CDATA[ | 80 <help><![CDATA[ |
| 75 **fgbio GroupReadsByUmi** | 81 **fgbio GroupReadsByUmi** |
| 76 | 82 |
| 77 Groups reads together that appear to have come from the same original molecule. Reads are grouped by template, and then templates are sorted by the 5’ mapping positions of the reads from the template, used from earliest mapping position to latest. Reads that have the same end positions are then sub-grouped by UMI sequence. | 83 Groups reads together that appear to have come from the same original molecule. Reads are grouped by template, and then templates are sorted by the 5’ mapping positions of the reads from the template, used from earliest mapping position to latest. Reads that have the same end positions are then sub-grouped by UMI sequence. |