Mercurial > repos > iuc > seqtk
view seqtk_hety.xml @ 2:f73729b62b51 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 2249d643284ee782d882cd200729a86a2c6bb744
author | iuc |
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date | Fri, 01 Jan 2016 14:49:42 -0500 |
parents | e0a0fd938de4 |
children | bc7d99f46a5d |
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<?xml version="1.0"?> <tool id="seqtk_hety" name="seqtk_hety" version="@WRAPPER_VERSION@.0"> <description>regional heterozygosity</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <command><![CDATA[seqtk hety -w $w -t $t $m $in_file | awk 'BEGIN{print "#chr\tstart\tend\tA\tB\tnum_het"}1' > $default]]></command> <inputs> <expand macro="in_faq"/> <param label="window size" help="(-w)" name="w" type="integer" value="50000"/> <param label="# start positions in a window" help="(-t)" name="t" type="integer" value="5"/> <param checked="false" label="treat lowercases as masked" help="(-m)" name="m" type="boolean" falsevalue="" truevalue="-m"/> </inputs> <outputs> <data format="tabular" hidden="false" name="default" label="Heterozygous regions in $in_file.name"/> </outputs> <tests> <test> <param name="in_file" value="seqtk_hety.fa"/> <param name="w" value="8"/> <output name="default" file="seqtk_hety.out" ftype="tabular"/> </test> </tests> <help><![CDATA[ **What it does** Reports on heterozygosity over a region :: >het_region ACTTTACATCGAGCMMMMMMMACAGTACTG As can be seen in the following output: :: #chr start end A B num_het het_region 0 8 0.00 8 0 het_region 8 9 0.00 8 0 het_region 9 10 0.00 8 0 het_region 10 11 0.00 8 0 het_region 11 12 0.00 8 0 het_region 12 13 0.00 8 0 het_region 13 14 0.00 8 0 het_region 14 15 1.00 8 1 het_region 15 16 2.00 8 2 het_region 16 17 3.00 8 3 het_region 17 18 4.00 8 4 het_region 18 19 5.00 8 5 het_region 19 20 6.00 8 6 het_region 20 21 7.00 8 7 het_region 21 22 7.00 8 7 het_region 22 23 6.00 8 6 het_region 23 24 5.00 8 5 het_region 24 25 4.00 8 4 het_region 25 26 3.00 8 3 het_region 26 27 2.00 8 2 het_region 27 28 1.00 8 1 het_region 28 29 0.00 8 0 het_region 29 30 0.00 1 0 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 @ATTRIBUTION@ ]]></help> <expand macro="citation" /> </tool>