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annotate seqtk_hety.xml @ 5:a09586d5149a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 83ecfe7d9bbf03c91f27ba18776352a1ebf8cf6f
author iuc
date Fri, 11 Jan 2019 05:15:20 -0500
parents ecf1c30da3a2
children 3da72230c066
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1 <?xml version="1.0"?>
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2 <tool id="seqtk_hety" name="seqtk_hety" version="@TOOL_VERSION@.1">
3
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3 <description>regional heterozygosity</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
5
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7 <expand macro="requirements">
a09586d5149a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 83ecfe7d9bbf03c91f27ba18776352a1ebf8cf6f
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8 <requirement type="package" version="@AWK_VERSION@">gawk</requirement>
a09586d5149a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 83ecfe7d9bbf03c91f27ba18776352a1ebf8cf6f
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9 </expand>
3
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10 <expand macro="stdio"/>
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11 <command><![CDATA[
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12 seqtk hety
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13 -w $w
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14 -t $t
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15 $m
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16 '$in_file' | awk 'BEGIN{print "#chr\tstart\tend\tA\tB\tnum_het"}1'
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17 > '$default'
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18 ]]></command>
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19 <inputs>
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20 <expand macro="in_faq"/>
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21 <param argument="-w" type="integer" value="50000" label="Window size" />
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22 <param argument="-t" type="integer" value="5" label="# start positions in a window" />
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23 <param argument="-m" type="boolean" truevalue="-m" falsevalue="" checked="false" label="Treat lowercases as masked" />
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24 </inputs>
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25 <outputs>
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26 <data name="default" format="tabular" label="Heterozygous regions in $in_file.name"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="in_file" value="seqtk_hety.fa"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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31 <param name="w" value="8"/>
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32 <output name="default" file="seqtk_hety.out" ftype="tabular"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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33 </test>
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34 <test>
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35 <param name="in_file" value="seqtk_hety.fa.gz" ftype="fasta.gz"/>
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36 <param name="w" value="8"/>
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37 <output name="default" file="seqtk_hety.out" ftype="tabular"/>
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38 </test>
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39 </tests>
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40 <help><![CDATA[
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41 **What it does**
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42
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43 Reports on heterozygosity over a region
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44
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45 ::
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46
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47 >het_region
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48 ACTTTACATCGAGCMMMMMMMACAGTACTG
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49
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50 As can be seen in the following output:
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51
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52 ::
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53
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54 #chr start end A B num_het
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55 het_region 0 8 0.00 8 0
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56 het_region 8 9 0.00 8 0
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57 het_region 9 10 0.00 8 0
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58 het_region 10 11 0.00 8 0
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59 het_region 11 12 0.00 8 0
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60 het_region 12 13 0.00 8 0
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61 het_region 13 14 0.00 8 0
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62 het_region 14 15 1.00 8 1
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63 het_region 15 16 2.00 8 2
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64 het_region 16 17 3.00 8 3
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65 het_region 17 18 4.00 8 4
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66 het_region 18 19 5.00 8 5
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67 het_region 19 20 6.00 8 6
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68 het_region 20 21 7.00 8 7
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69 het_region 21 22 7.00 8 7
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70 het_region 22 23 6.00 8 6
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71 het_region 23 24 5.00 8 5
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72 het_region 24 25 4.00 8 4
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73 het_region 25 26 3.00 8 3
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74 het_region 26 27 2.00 8 2
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75 het_region 27 28 1.00 8 1
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76 het_region 28 29 0.00 8 0
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77 het_region 29 30 0.00 1 0
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78
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79 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
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80
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81 @ATTRIBUTION@
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82 ]]></help>
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83 <expand macro="citation" />
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84 </tool>