Mercurial > repos > iuc > seqtk
comparison seqtk_listhet.xml @ 0:e0a0fd938de4 draft
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| author | iuc |
|---|---|
| date | Thu, 05 Feb 2015 11:52:40 -0500 |
| parents | |
| children | f73729b62b51 |
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| -1:000000000000 | 0:e0a0fd938de4 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool id="seqtk_listhet" name="seqtk_listhet" version="@WRAPPER_VERSION@.0"> | |
| 3 <description>extract the position of each het</description> | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements"/> | |
| 8 <expand macro="stdio"/> | |
| 9 <command><![CDATA[seqtk listhet $in_file | awk 'BEGIN{print "#chr\tposition\tbase"}1' > $default]]></command> | |
| 10 <inputs> | |
| 11 <expand macro="in_faq"/> | |
| 12 </inputs> | |
| 13 <outputs> | |
| 14 <data format="tabular" hidden="false" name="default" label="Positions of heterozygous bases in $in_file.name"/> | |
| 15 </outputs> | |
| 16 <tests> | |
| 17 <test> | |
| 18 <param name="in_file" value="seqtk_listhet.fa"/> | |
| 19 <output name="default" file="seqtk_listhet.out" ftype="tabular"/> | |
| 20 </test> | |
| 21 </tests> | |
| 22 <help><![CDATA[ | |
| 23 **What it does** | |
| 24 | |
| 25 Lists regions of heterozygosity. | |
| 26 | |
| 27 :: | |
| 28 | |
| 29 >ambig | |
| 30 ACGTMRWSYKVHDBN | |
| 31 | |
| 32 The seqtk suite recognises MRWSYK: | |
| 33 | |
| 34 :: | |
| 35 | |
| 36 #chr position base | |
| 37 ambig 5 M | |
| 38 ambig 6 R | |
| 39 ambig 7 W | |
| 40 ambig 8 S | |
| 41 ambig 9 Y | |
| 42 ambig 10 K | |
| 43 | |
| 44 | |
| 45 @ATTRIBUTION@ | |
| 46 ]]></help> | |
| 47 </tool> |