Mercurial > repos > iuc > seqtk
comparison seqtk_hety.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_hety" name="seqtk_hety" version="@WRAPPER_VERSION@.0"> | |
| 3 <description>regional heterozygosity</description> | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements"/> | |
| 8 <expand macro="stdio"/> | |
| 9 <command><![CDATA[seqtk hety -w $w | |
| 10 -t $t | |
| 11 $m | |
| 12 $in_file | awk 'BEGIN{print "#chr\tstart\tend\tA\tB\tnum_het"}1' | |
| 13 > $default]]></command> | |
| 14 <inputs> | |
| 15 <expand macro="in_faq"/> | |
| 16 <param label="window size" help="(-w)" name="w" type="integer" value="50000"/> | |
| 17 <param label="# start positions in a window" help="(-t)" name="t" type="integer" value="5"/> | |
| 18 <param checked="false" label="treat lowercases as masked" help="(-m)" name="m" type="boolean" falsevalue="" truevalue="-m"/> | |
| 19 </inputs> | |
| 20 <outputs> | |
| 21 <data format="tabular" hidden="false" name="default" label="Heterozygous regions in $in_file.name"/> | |
| 22 </outputs> | |
| 23 <tests> | |
| 24 <test> | |
| 25 <param name="in_file" value="seqtk_hety.fa"/> | |
| 26 <param name="w" value="8"/> | |
| 27 <output name="default" file="seqtk_hety.out" ftype="tabular"/> | |
| 28 </test> | |
| 29 </tests> | |
| 30 <help><![CDATA[ | |
| 31 **What it does** | |
| 32 | |
| 33 Reports on heterozygosity over a region | |
| 34 | |
| 35 :: | |
| 36 | |
| 37 >het_region | |
| 38 ACTTTACATCGAGCMMMMMMMACAGTACTG | |
| 39 | |
| 40 As can be seen in the following output: | |
| 41 | |
| 42 :: | |
| 43 | |
| 44 #chr start end A B num_het | |
| 45 het_region 0 8 0.00 8 0 | |
| 46 het_region 8 9 0.00 8 0 | |
| 47 het_region 9 10 0.00 8 0 | |
| 48 het_region 10 11 0.00 8 0 | |
| 49 het_region 11 12 0.00 8 0 | |
| 50 het_region 12 13 0.00 8 0 | |
| 51 het_region 13 14 0.00 8 0 | |
| 52 het_region 14 15 1.00 8 1 | |
| 53 het_region 15 16 2.00 8 2 | |
| 54 het_region 16 17 3.00 8 3 | |
| 55 het_region 17 18 4.00 8 4 | |
| 56 het_region 18 19 5.00 8 5 | |
| 57 het_region 19 20 6.00 8 6 | |
| 58 het_region 20 21 7.00 8 7 | |
| 59 het_region 21 22 7.00 8 7 | |
| 60 het_region 22 23 6.00 8 6 | |
| 61 het_region 23 24 5.00 8 5 | |
| 62 het_region 24 25 4.00 8 4 | |
| 63 het_region 25 26 3.00 8 3 | |
| 64 het_region 26 27 2.00 8 2 | |
| 65 het_region 27 28 1.00 8 1 | |
| 66 het_region 28 29 0.00 8 0 | |
| 67 het_region 29 30 0.00 1 0 | |
| 68 | |
| 69 If you know what A and B are measures of, please `submit an issue <https://github.com/galaxyproject/tools-iuc/issues>`__ and it will be corrected | |
| 70 | |
| 71 @ATTRIBUTION@ | |
| 72 ]]></help> | |
| 73 </tool> |