Mercurial > repos > wolma > mimodd
annotate bamsort.xml @ 21:c46406466625 draft
Uploaded
| author | wolma |
|---|---|
| date | Sat, 11 Jun 2016 19:10:44 -0400 |
| parents | 93db2f9bca12 |
| children | 5db0545b9004 |
| rev | line source |
|---|---|
|
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"/> | |
| 21 | 7 <version_command>python3 -m MiModD version -q</version_command> |
| 0 | 8 <command> |
| 21 | 9 python3 -m 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 |