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annotate seqtk_mutfa.xml @ 16:48a51c72f5e7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
author iuc
date Wed, 17 Oct 2018 05:58:58 -0400
parents 16f2535c08bf
children 069c8f0695ee
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1 <?xml version="1.0"?>
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2 <tool id="seqtk_mutfa" name="seqtk_mutfa" version="@WRAPPER_VERSION@.0">
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3 <description>point mutate FASTA at specified positions</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 mutfa
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11 '$in_file'
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12 '$in_snp'
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13 @CONDITIONAL_GZIP_OUT@
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14 ]]></command>
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15 <inputs>
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16 <expand macro="in_faq"/>
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17 <param name="in_snp" type="data" format="tabular" label="Input SNP file"/>
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18 </inputs>
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19 <outputs>
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20 <data name="default" format_source="in_file" label="Mutated $in_file.name"/>
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="in_file" value="seqtk_mutfa.fa"/>
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25 <param name="in_snp" value="seqtk_mutfa.snp"/>
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26 <output name="default" file="seqtk_mutfa.out" ftype="fasta"/>
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27 </test>
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28 <test>
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29 <param name="in_file" value="seqtk_mutfa.fa.gz" ftype="fasta.gz"/>
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30 <param name="in_snp" value="seqtk_mutfa.snp"/>
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31 <output name="default" file="seqtk_mutfa.out.gz" ftype="fasta.gz"/>
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32 </test>
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33 </tests>
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34 <help><![CDATA[
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35 **What it does**
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36
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37 the SNP inputs consist of 4 columns: chromosome, 1-based-pos, any, base-changed-to.
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38
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39 ::
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40
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41 # Input fasta
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42 >test0
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43 ACTGACTGAA
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44
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45 # Input SNP file
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46 test0 1 . G
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47 test0 4 . A
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48
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49 This will effect the desired mutations in the output file
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50
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51 ::
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52
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53 # Output result
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54 >test0
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55 GCTAACTGAA
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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>