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comparison seqtk_hety.xml @ 3:bc7d99f46a5d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
author iuc
date Mon, 05 Jun 2017 13:27:11 -0400
parents f73729b62b51
children ecf1c30da3a2
comparison
equal deleted inserted replaced
2:f73729b62b51 3:bc7d99f46a5d
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="seqtk_hety" name="seqtk_hety" version="@WRAPPER_VERSION@.0"> 2 <tool id="seqtk_hety" name="seqtk_hety" version="@WRAPPER_VERSION@.0">
3 <description>regional heterozygosity</description> 3 <description>regional heterozygosity</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <expand macro="stdio"/> 8 <expand macro="stdio"/>
9 <command><![CDATA[seqtk hety -w $w 9 <command><![CDATA[
10 seqtk hety
11 -w $w
10 -t $t 12 -t $t
11 $m 13 $m
12 $in_file | awk 'BEGIN{print "#chr\tstart\tend\tA\tB\tnum_het"}1' 14 '$in_file' | awk 'BEGIN{print "#chr\tstart\tend\tA\tB\tnum_het"}1'
13 > $default]]></command> 15 > '$default'
14 <inputs> 16 ]]></command>
15 <expand macro="in_faq"/> 17 <inputs>
16 <param label="window size" help="(-w)" name="w" type="integer" value="50000"/> 18 <expand macro="in_faq"/>
17 <param label="# start positions in a window" help="(-t)" name="t" type="integer" value="5"/> 19 <param argument="-w" type="integer" value="50000" label="Window size" />
18 <param checked="false" label="treat lowercases as masked" help="(-m)" name="m" type="boolean" falsevalue="" truevalue="-m"/> 20 <param argument="-t" type="integer" value="5" label="# start positions in a window" />
19 </inputs> 21 <param argument="-m" type="boolean" truevalue="-m" falsevalue="" checked="false" label="Treat lowercases as masked" />
20 <outputs> 22 </inputs>
21 <data format="tabular" hidden="false" name="default" label="Heterozygous regions in $in_file.name"/> 23 <outputs>
22 </outputs> 24 <data name="default" format="tabular" label="Heterozygous regions in $in_file.name"/>
23 <tests> 25 </outputs>
24 <test> 26 <tests>
25 <param name="in_file" value="seqtk_hety.fa"/> 27 <test>
26 <param name="w" value="8"/> 28 <param name="in_file" value="seqtk_hety.fa"/>
27 <output name="default" file="seqtk_hety.out" ftype="tabular"/> 29 <param name="w" value="8"/>
28 </test> 30 <output name="default" file="seqtk_hety.out" ftype="tabular"/>
29 </tests> 31 </test>
30 <help><![CDATA[ 32 </tests>
33 <help><![CDATA[
31 **What it does** 34 **What it does**
32 35
33 Reports on heterozygosity over a region 36 Reports on heterozygosity over a region
34 37
35 :: 38 ::
67 het_region 29 30 0.00 1 0 70 het_region 29 30 0.00 1 0
68 71
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 72 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 73
71 @ATTRIBUTION@ 74 @ATTRIBUTION@
72 ]]></help> 75 ]]></help>
73 <expand macro="citation" /> 76 <expand macro="citation" />
74 </tool> 77 </tool>