Mercurial > repos > iuc > seqtk

annotate seqtk_cutN.xml @ 18:1d63dbcecb10 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 50a0bd6d783a69e7303363a31130134767493e66"
author iuc
date Fri, 06 Sep 2019 09:09:35 -0400
parents 069c8f0695ee
children 8f26884c60b6
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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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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 @CONDITIONAL_GZIP_OUT@
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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" />
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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"/>
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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 <test>
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33 <param name="in_file" value="seqtk_cutn.fa.gz" ftype="fasta.gz"/>
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34 <param name="n" value="1"/>
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35 <output name="default" file="seqtk_cutn.out.gz" ftype="fasta.gz"/>
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36 </test>
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37 </tests>
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38 <help><![CDATA[
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39 **What it does**
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40
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41 Splits long sequences with runs of Ns
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42
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43 ::
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44
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45 >test
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46 AACTGATCGATCGATCGNNNNNNNNNNNACATG
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47
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48 This will be split into the component sequences without the ambiguity.
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49
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50 ::
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51
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52 >test:1-17
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53 AACTGATCGATCGATCG
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54 >test:29-33
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55 ACATG
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56
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57 @ATTRIBUTION@
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58 ]]></help>
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59 <expand macro="citation" />
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60 </tool>