Mercurial > repos > wolma > mimodd_bamsort
changeset 0:074a654fd253 draft
Uploaded
author | wolma |
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date | Wed, 13 Aug 2014 07:14:20 -0400 |
parents | |
children | 73644d9cb40a |
files | bamsort.xml |
diffstat | 1 files changed, 39 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamsort.xml Wed Aug 13 07:14:20 2014 -0400 @@ -0,0 +1,39 @@ +<tool id="bamsort" name="Sort BAM file"> + <description>Sort a BAM file by coordinates (or names) of the mapped reads</description> + <requirements> + <requirement type="package" version="0.1.3">mimodd</requirement> + </requirements> + <command> + mimodd sort $inputfile -o $output --oformat $oformat $by_name + </command> + + <inputs> + <param name="inputfile" type="data" format="bam" label="Input file to sort" /> + <param name="by_name" type="boolean" truevalue = "-n" falsevalue ="" label="Sort by read names instead of coordinates" checked = "false" help="A less common option, but necessary, e.g., if you want to re-align sorted output from a previous run of the Snap Align Tool." /> + <param name="oformat" type="boolean" truevalue = "sam" falsevalue = "bam" label = "Output in uncompressed SAM format" checked = "false" /> + </inputs> + + <outputs> + <data name="output" format="bam" label="Sorted output from MiModd ${tool.name} on ${on_string}"> + <change_format> + <when input="oformat" value="sam" format="sam" /> + </change_format> + </data> + </outputs> + +<help> +.. class:: infomark + + **What it does** + +The tool sorts a BAM file of aligned reads, typically by the reference genome coordinates that the reads have been mapped to. + +Coordinate-sorted input files are expected by the downstream MiModD tools *Variant Calling and Coverage Analysis* and *Deletion prediction*. + +Note, however, that the *SNAP Read Alignment* produces coordinate-sorted output by default and it is only necessary to sort files that come from other sources or from *SNAP Read Alignment* jobs with a custom sort order. + +The option *Sort by read names instead of coordinates* is useful if you want to re-align coordinate-sorted paired-end data. In *paired-end mode*, the *SNAP Read Alignment* tool expects the reads in the input file to be arranged in read pairs, i.e., the forward read information of a pair must be followed immediately by its reverse mate information, which is typically not the case in coordinate-sorted files. Resorting such files by read names fixes this problem. + +</help> +</tool> +