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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>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <command><![CDATA[seqtk listhet $in_file | awk 'BEGIN{print "#chr\tposition\tbase"}1' > $default]]></command>
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10 <inputs>
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11 <expand macro="in_faq"/>
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12 </inputs>
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13 <outputs>
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14 <data format="tabular" hidden="false" name="default" label="Positions of heterozygous bases in $in_file.name"/>
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15 </outputs>
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16 <tests>
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17 <test>
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18 <param name="in_file" value="seqtk_listhet.fa"/>
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19 <output name="default" file="seqtk_listhet.out" ftype="tabular"/>
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20 </test>
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21 </tests>
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22 <help><![CDATA[
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23 **What it does**
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24
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25 Lists regions of heterozygosity.
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26
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27 ::
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28
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29 >ambig
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30 ACGTMRWSYKVHDBN
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31
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32 The seqtk suite recognises MRWSYK:
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33
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34 ::
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35
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36 #chr position base
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37 ambig 5 M
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38 ambig 6 R
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39 ambig 7 W
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40 ambig 8 S
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41 ambig 9 Y
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42 ambig 10 K
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43
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44
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45 @ATTRIBUTION@
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46 ]]></help>
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47 </tool>
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