Mercurial > repos > iuc > seqtk
comparison seqtk_sample.xml @ 0:e0a0fd938de4 draft
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| author | iuc |
|---|---|
| date | Thu, 05 Feb 2015 11:52:40 -0500 |
| parents | |
| children | 61718851f199 |
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| -1:000000000000 | 0:e0a0fd938de4 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool id="seqtk_sample" name="seqtk_sample" version="@WRAPPER_VERSION@.0"> | |
| 3 <description/> | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements"/> | |
| 8 <expand macro="stdio"/> | |
| 9 <command><![CDATA[seqtk sample -s $s | |
| 10 $in_file | |
| 11 $subsample_size | |
| 12 > $default]]></command> | |
| 13 <inputs> | |
| 14 <expand macro="in_faq" /> | |
| 15 <param label="RNG seed" help="(-s)" name="s" type="integer" value="4"/> | |
| 16 <param label="Subsample (decimal fraction or number)" name="subsample_size" type="integer" value="100"/> | |
| 17 </inputs> | |
| 18 <outputs> | |
| 19 <data format_source="in_file" hidden="false" name="default" label="Subsample of reads from $in_file.name"/> | |
| 20 </outputs> | |
| 21 <tests> | |
| 22 <test> | |
| 23 <param name="in_file" value="seqtk_sample.fa"/> | |
| 24 <param name="subsample_size" value="4"/> | |
| 25 <param name="s" value="4"/> | |
| 26 <output name="default" file="seqtk_sample.out" ftype="fasta"/> | |
| 27 </test> | |
| 28 </tests> | |
| 29 <help><![CDATA[ | |
| 30 **What it does** | |
| 31 | |
| 32 Takes a random subsample of fasta or fastq sequences. The RNG is seedable to allow for reproducible results, and defaults to `4 <http://xkcd.com/221/>`__. | |
| 33 | |
| 34 The subsample size can be a decimal fraction <=1, where 1 implies 100% of the reads should be used. If a number >1 is provided, that many reads will be taken from the dataset. | |
| 35 | |
| 36 @ATTRIBUTION@ | |
| 37 ]]></help> | |
| 38 </tool> |