Mercurial > repos > wolma > mimodd
comparison bamsort.xml @ 5:bdd1995c9e66
upgrade to mimodd version 0.1.6.1
| author | Wolfgang Maier |
|---|---|
| date | Tue, 28 Jul 2015 23:21:11 +0200 |
| parents | 72d20758ba2c |
| children | 85214e4428fd |
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| 4:ffee8534a5c4 | 5:bdd1995c9e66 |
|---|---|
| 1 <tool id="bamsort" name="Sort BAM file"> | 1 <tool id="bamsort" name="Sort BAM file" version="0.1.6.1"> |
| 2 <description>Sort a BAM file by coordinates (or names) of the mapped reads</description> | 2 <description>Sort a BAM file by coordinates (or names) of the mapped reads</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>toolshed_macros.xml</import> | 4 <import>toolshed_macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
| 7 <version_command>mimodd version -q</version_command> | 7 <version_command>mimodd version -q</version_command> |
| 8 <command> | 8 <command> |
| 9 mimodd sort "$inputfile" -o "$output" --oformat $oformat $by_name | 9 mimodd sort "$input.ifile" -o "$output" --iformat $input.iformat --oformat $oformat $by_name |
| 10 </command> | 10 </command> |
| 11 | 11 |
| 12 <inputs> | 12 <inputs> |
| 13 <param name="inputfile" type="data" format="bam" label="Input file to sort" /> | 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> | |
| 14 <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." /> | 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." /> |
| 15 <param name="oformat" type="boolean" truevalue = "sam" falsevalue = "bam" label = "Output in uncompressed SAM format" checked = "false" /> | |
| 16 </inputs> | 30 </inputs> |
| 17 | 31 |
| 18 <outputs> | 32 <outputs> |
| 19 <data name="output" format="bam" label="Sorted output from MiModd ${tool.name} on ${on_string}"> | 33 <data name="output" format="bam" label="Sorted output from MiModd ${tool.name} on ${on_string}"> |
| 20 <change_format> | 34 <change_format> |