Mercurial > repos > iuc > seqtk

annotate seqtk_listhet.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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a09586d5149a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 83ecfe7d9bbf03c91f27ba18776352a1ebf8cf6f
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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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4 <macros>
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5 <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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6 </macros>
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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 listhet
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13 '$in_file' | awk 'BEGIN{print "#chr\tposition\tbase"}1'
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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14 > '$default'
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15 ]]></command>
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16 <inputs>
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17 <expand macro="in_faq"/>
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18 </inputs>
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19 <outputs>
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20 <data name="default" format="tabular" label="Positions of heterozygous bases 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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21 </outputs>
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22 <tests>
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23 <test>
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24 <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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25 <output name="default" file="seqtk_listhet.out" ftype="tabular"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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26 </test>
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27 <test>
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28 <param name="in_file" value="seqtk_listhet.fa.gz" ftype="fasta.gz"/>
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29 <output name="default" file="seqtk_listhet.out" ftype="tabular"/>
ecf1c30da3a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
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30 </test>
3
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31 </tests>
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32 <help><![CDATA[
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33 **What it does**
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34
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35 Lists regions of heterozygosity.
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36
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37 ::
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38
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39 >ambig
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40 ACGTMRWSYKVHDBN
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41
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42 The seqtk suite recognises MRWSYK:
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43
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44 ::
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45
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46 #chr position base
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47 ambig 5 M
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48 ambig 6 R
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49 ambig 7 W
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50 ambig 8 S
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51 ambig 9 Y
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52 ambig 10 K
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53
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54
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55 @ATTRIBUTION@
3
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56 ]]></help>
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57 <expand macro="citation" />
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58 </tool>