Mercurial > repos > iuc > seqtk

annotate seqtk_cutN.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_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[
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10 seqtk cutN
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11 -n $n
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12 -p $p
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13 $g
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14 '$in_file'
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15 > '$default'
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16 ]]></command>
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17 <inputs>
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18 <expand macro="in_faq"/>
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19 <param argument="-n" type="integer" value="1000" label="Minimum size of N tract" />
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20 <param argument="-p" type="integer" value="10" label="Penalty for a non-N" />
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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21 <param argument="-g" type="boolean" truevalue="-g" falsevalue="" checked="false" label="Print gaps only, no sequence" />
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22 </inputs>
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23 <outputs>
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24 <data name="default" format_source="in_file" label="$in_file.name split on N runs longer than $n"/>
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="in_file" value="seqtk_cutn.fa"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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29 <param name="n" value="1"/>
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30 <output name="default" file="seqtk_cutn.out" ftype="fasta"/>
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31 </test>
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32 </tests>
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33 <help><![CDATA[
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34 **What it does**
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35
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36 Splits long sequences with runs of Ns
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37
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38 ::
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39
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40 >test
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41 AACTGATCGATCGATCGNNNNNNNNNNNACATG
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42
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43 This will be split into the component sequences without the ambiguity.
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44
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45 ::
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46
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47 >test:1-17
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48 AACTGATCGATCGATCG
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49 >test:29-33
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50 ACATG
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51
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52 @ATTRIBUTION@
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53 ]]></help>
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54 <expand macro="citation" />
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55 </tool>