Mercurial > repos > iuc > seqtk

annotate seqtk_listhet.xml @ 8:3da72230c066 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 690c73637e3b8be3a52fe3afc8ba6436c4bab46f"
author iuc
date Thu, 14 Oct 2021 09:22:39 +0000
parents a09586d5149a
children 4b494533146a
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1 <?xml version="1.0"?>
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2 <tool id="seqtk_listhet" name="seqtk_listhet" version="@TOOL_VERSION@.1">
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3 <description>extract the position of each het</description>
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3da72230c066 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 690c73637e3b8be3a52fe3afc8ba6436c4bab46f"
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4 <expand macro="bio_tools"/>
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5 <macros>
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6 <import>macros.xml</import>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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7 </macros>
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8 <expand macro="requirements">
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9 <requirement type="package" version="@AWK_VERSION@">gawk</requirement>
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10 </expand>
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11 <expand macro="stdio"/>
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12 <command><![CDATA[
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13 seqtk listhet
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14 '$in_file' | awk 'BEGIN{print "#chr\tposition\tbase"}1'
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15 > '$default'
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16 ]]></command>
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17 <inputs>
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18 <expand macro="in_faq"/>
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19 </inputs>
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20 <outputs>
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21 <data name="default" format="tabular" label="Positions of heterozygous bases in $in_file.name"/>
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="in_file" value="seqtk_listhet.fa"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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26 <output name="default" file="seqtk_listhet.out" ftype="tabular"/>
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27 </test>
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28 <test>
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29 <param name="in_file" value="seqtk_listhet.fa.gz" ftype="fasta.gz"/>
ecf1c30da3a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
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30 <output name="default" file="seqtk_listhet.out" ftype="tabular"/>
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31 </test>
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32 </tests>
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33 <help><![CDATA[
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34 **What it does**
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35
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36 Lists regions of heterozygosity.
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37
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38 ::
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39
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40 >ambig
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41 ACGTMRWSYKVHDBN
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42
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43 The seqtk suite recognises MRWSYK:
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44
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45 ::
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46
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47 #chr position base
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48 ambig 5 M
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49 ambig 6 R
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50 ambig 7 W
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51 ambig 8 S
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52 ambig 9 Y
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53 ambig 10 K
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54
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55
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56 @ATTRIBUTION@
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57 ]]></help>
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58 <expand macro="citation" />
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59 </tool>