Mercurial > repos > iuc > seqtk

annotate seqtk_listhet.xml @ 4:ecf1c30da3a2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
author iuc
date Wed, 17 Oct 2018 05:59:21 -0400
parents bc7d99f46a5d
children a09586d5149a
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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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3 <description>extract the position of each het</description>
bc7d99f46a5d 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>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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6 </macros>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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7 <expand macro="requirements"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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8 <expand macro="stdio"/>
bc7d99f46a5d 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"/>
bc7d99f46a5d 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"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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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 <test>
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26 <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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27 <output name="default" file="seqtk_listhet.out" ftype="tabular"/>
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28 </test>
3
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29 </tests>
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30 <help><![CDATA[
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31 **What it does**
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32
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33 Lists regions of heterozygosity.
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34
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35 ::
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36
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37 >ambig
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38 ACGTMRWSYKVHDBN
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39
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40 The seqtk suite recognises MRWSYK:
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41
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42 ::
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43
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44 #chr position base
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45 ambig 5 M
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46 ambig 6 R
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47 ambig 7 W
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48 ambig 8 S
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49 ambig 9 Y
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50 ambig 10 K
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51
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52
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53 @ATTRIBUTION@
3
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54 ]]></help>
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55 <expand macro="citation" />
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56 </tool>