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1 <?xml version="1.0"?>
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2 <tool id="seqtk_cutN" name="seqtk_cutN" version="@WRAPPER_VERSION@.0">
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3 <description>cut sequence at long N</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 cutN -n $n
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10 -p $p
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11 $g
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12 $in_file
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13 > $default]]></command>
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14 <inputs>
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15 <expand macro="in_faq"/>
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16 <param label="min size of N tract" help="(-n)" name="n" type="integer" value="1000"/>
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17 <param label="penalty for a non-N" help="(-p)" name="p" type="integer" value="10"/>
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18 <param checked="false" label="print gaps only, no sequence" help="(-g)" name="g" type="boolean" falsevalue="" truevalue="-g"/>
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19 </inputs>
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20 <outputs>
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21 <data format_source="in_file" hidden="false" name="default" label="$in_file.name split on N runs longer than $n"/>
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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_cutn.fa"/>
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26 <param name="n" value="1"/>
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27 <output name="default" file="seqtk_cutn.out" ftype="fasta"/>
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28 </test>
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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 Splits long sequences with runs of Ns
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34
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35 ::
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36
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37 >test
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38 AACTGATCGATCGATCGNNNNNNNNNNNACATG
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39
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40 This will be split into the component sequences without the ambiguity.
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41
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42 ::
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43
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44 >test:1-17
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45 AACTGATCGATCGATCG
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46 >test:29-33
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47 ACATG
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48
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49
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50 @ATTRIBUTION@
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51 ]]></help>
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52 </tool>
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