Mercurial > repos > iuc > seqtk

annotate seqtk_cutN.xml @ 8:3da72230c066 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 690c73637e3b8be3a52fe3afc8ba6436c4bab46f"
author iuc
date Thu, 14 Oct 2021 09:22:39 +0000
parents a09586d5149a
children 4b494533146a
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1 <?xml version="1.0"?>
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2 <tool id="seqtk_cutN" name="seqtk_cutN" version="@TOOL_VERSION@.1">
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3 <description>cut sequence at long N</description>
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3da72230c066 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 690c73637e3b8be3a52fe3afc8ba6436c4bab46f"
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4 <expand macro="bio_tools"/>
3
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <expand macro="stdio"/>
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10 <command><![CDATA[
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11 seqtk cutN
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12 -n $n
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13 -p $p
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14 $g
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15 '$in_file'
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16 @CONDITIONAL_GZIP_OUT@
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17 ]]></command>
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18 <inputs>
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19 <expand macro="in_faq"/>
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20 <param argument="-n" type="integer" value="1000" label="Minimum size of N tract" />
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21 <param argument="-p" type="integer" value="10" label="Penalty for a non-N" />
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22 <param argument="-g" type="boolean" truevalue="-g" falsevalue="" checked="false" label="Print gaps only, no sequence" />
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23 </inputs>
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24 <outputs>
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25 <data name="default" format_source="in_file" label="$in_file.name split on N runs longer than $n"/>
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="in_file" value="seqtk_cutn.fa"/>
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30 <param name="n" value="1"/>
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31 <output name="default" file="seqtk_cutn.out" ftype="fasta"/>
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32 </test>
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33 <test>
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34 <param name="in_file" value="seqtk_cutn.fa.gz" ftype="fasta.gz"/>
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35 <param name="n" value="1"/>
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36 <output name="default" file="seqtk_cutn.out.gz" ftype="fasta.gz"/>
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37 </test>
3
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38 </tests>
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39 <help><![CDATA[
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40 **What it does**
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41
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42 Splits long sequences with runs of Ns
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43
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44 ::
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45
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46 >test
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47 AACTGATCGATCGATCGNNNNNNNNNNNACATG
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48
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49 This will be split into the component sequences without the ambiguity.
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50
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51 ::
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52
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53 >test:1-17
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54 AACTGATCGATCGATCG
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55 >test:29-33
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56 ACATG
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57
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58 @ATTRIBUTION@
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59 ]]></help>
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60 <expand macro="citation" />
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61 </tool>