Mercurial > repos > wolma > mimodd
annotate bamsort.xml @ 15:92bd325c70da draft
Uploaded
author | wolma |
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date | Mon, 25 Apr 2016 17:55:19 -0400 |
parents | 93db2f9bca12 |
children | c46406466625 |
rev | line source |
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9
93db2f9bca12
upgrade to v0.1.7.2
Wolfgang Maier wolfgang.maier@biologie.uni-freiburg.de
parents:
8
diff
changeset
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1 <tool id="bamsort" name="Sort BAM file" version="0.1.7.2"> |
0 | 2 <description>Sort a BAM file by coordinates (or names) of the mapped reads</description> |
2 | 3 <macros> |
4 <import>toolshed_macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"/> | |
0 | 7 <version_command>mimodd version -q</version_command> |
8 <command> | |
5 | 9 mimodd sort "$input.ifile" -o "$output" --iformat $input.iformat --oformat $oformat $by_name |
0 | 10 </command> |
11 | |
12 <inputs> | |
5 | 13 <conditional name="input"> |
14 <param name="iformat" type="select" label = "Input data format"> | |
15 <option value="bam">bam</option> | |
16 <option value="sam">sam</option> | |
17 </param> | |
18 <when value="bam"> | |
19 <param name="ifile" type="data" format="bam" label="BAM input file to sort" /> | |
20 </when> | |
21 <when value="sam"> | |
22 <param name="ifile" type="data" format="sam" label="SAM input file to sort" /> | |
23 </when> | |
24 </conditional> | |
25 <param name="oformat" type="select" label = "Output format for the sorted data"> | |
26 <option value="bam">bam</option> | |
27 <option value="sam">sam</option> | |
28 </param> | |
0 | 29 <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." /> |
30 </inputs> | |
31 | |
32 <outputs> | |
33 <data name="output" format="bam" label="Sorted output from MiModd ${tool.name} on ${on_string}"> | |
34 <change_format> | |
35 <when input="oformat" value="sam" format="sam" /> | |
36 </change_format> | |
37 </data> | |
38 </outputs> | |
39 | |
40 <help> | |
41 .. class:: infomark | |
42 | |
43 **What it does** | |
44 | |
45 The tool sorts a BAM file of aligned reads, typically by the reference genome coordinates that the reads have been mapped to. | |
46 | |
47 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. | |
48 | |
49 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. | |
50 | |
51 </help> | |
52 </tool> | |
53 |