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annotate seqtk_listhet.xml @ 15:16f2535c08bf 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 13:26:30 -0400
parents 55e75a28fde7
children 48a51c72f5e7
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1 <?xml version="1.0"?>
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2 <tool id="seqtk_listhet" name="seqtk_listhet" version="@WRAPPER_VERSION@.0">
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16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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3 <description>extract the position of each het</description>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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4 <macros>
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5 <import>macros.xml</import>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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6 </macros>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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7 <expand macro="requirements"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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8 <expand macro="stdio"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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9 <command><![CDATA[
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10 seqtk listhet
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11 '$in_file' | awk 'BEGIN{print "#chr\tposition\tbase"}1'
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12 > '$default'
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13 ]]></command>
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14 <inputs>
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15 <expand macro="in_faq"/>
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16 </inputs>
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17 <outputs>
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18 <data name="default" format="tabular" label="Positions of heterozygous bases in $in_file.name"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="in_file" value="seqtk_listhet.fa"/>
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23 <output name="default" file="seqtk_listhet.out" ftype="tabular"/>
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24 </test>
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25 </tests>
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26 <help><![CDATA[
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27 **What it does**
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28
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29 Lists regions of heterozygosity.
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30
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31 ::
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32
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33 >ambig
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34 ACGTMRWSYKVHDBN
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35
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36 The seqtk suite recognises MRWSYK:
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37
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38 ::
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39
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40 #chr position base
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41 ambig 5 M
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42 ambig 6 R
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43 ambig 7 W
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44 ambig 8 S
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45 ambig 9 Y
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46 ambig 10 K
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47
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48
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49 @ATTRIBUTION@
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50 ]]></help>
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51 <expand macro="citation" />
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52 </tool>