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comparison bamsort.xml @ 0:099d2c4d8007 draft

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author wolma
date Sat, 13 Dec 2014 17:19:46 -0500
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1 <tool id="bamsort" name="Sort BAM file">
2 <description>Sort a BAM file by coordinates (or names) of the mapped reads</description>
3 <requirements>
4 <requirement type="package" version="0.1.5">mimodd</requirement>
5 </requirements>
6 <version_command>mimodd version -q</version_command>
7 <command>
8 mimodd sort $inputfile -o $output --oformat $oformat $by_name
9 </command>
10
11 <inputs>
12 <param name="inputfile" type="data" format="bam" label="Input file to sort" />
13 <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." />
14 <param name="oformat" type="boolean" truevalue = "sam" falsevalue = "bam" label = "Output in uncompressed SAM format" checked = "false" />
15 </inputs>
16
17 <outputs>
18 <data name="output" format="bam" label="Sorted output from MiModd ${tool.name} on ${on_string}">
19 <change_format>
20 <when input="oformat" value="sam" format="sam" />
21 </change_format>
22 </data>
23 </outputs>
24
25 <help>
26 .. class:: infomark
27
28 **What it does**
29
30 The tool sorts a BAM file of aligned reads, typically by the reference genome coordinates that the reads have been mapped to.
31
32 Coordinate-sorted input files are expected by most downstream MiModD tools, but note 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.
33
34 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.
35
36 </help>
37 </tool>
38