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annotate seqtk_mutfa.xml @ 22:f2a792351212 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 75d5141110314addc160504e0a1f9cd66443de66
author iuc
date Wed, 16 Oct 2024 09:08:17 +0000
parents 8f26884c60b6
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1 <?xml version="1.0"?>
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2 <tool id="seqtk_mutfa" name="seqtk_mutfa" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
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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="bio_tools"/>
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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 mutfa
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12 '$in_file'
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13 '$in_snp'
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14 @CONDITIONAL_GZIP_OUT@
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15 ]]></command>
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16 <inputs>
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17 <expand macro="in_faq"/>
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18 <param name="in_snp" type="data" format="tabular" label="Input SNP file"/>
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19 </inputs>
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20 <outputs>
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21 <data name="default" format_source="in_file" label="${tool.name} on ${on_string}: Mutated"/>
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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_mutfa.fa"/>
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26 <param name="in_snp" value="seqtk_mutfa.snp"/>
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27 <output name="default" file="seqtk_mutfa.out" ftype="fasta"/>
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28 </test>
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29 <test>
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30 <param name="in_file" value="seqtk_mutfa.fa.gz" ftype="fasta.gz"/>
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31 <param name="in_snp" value="seqtk_mutfa.snp"/>
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32 <output name="default" file="seqtk_mutfa.out.gz" ftype="fasta.gz"/>
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33 </test>
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34 </tests>
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35 <help><![CDATA[
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36 **What it does**
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37
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38 the SNP inputs consist of 4 columns: chromosome, 1-based-pos, any, base-changed-to.
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39
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40 ::
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41
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42 # Input fasta
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43 >test0
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44 ACTGACTGAA
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45
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46 # Input SNP file
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47 test0 1 . G
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48 test0 4 . A
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49
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50 This will effect the desired mutations in the output file
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51
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52 ::
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53
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54 # Output result
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55 >test0
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56 GCTAACTGAA
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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>