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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[seqtk mutfa
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10 $in_file $in_snp
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11 > $default]]></command>
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12 <inputs>
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13 <expand macro="in_faq"/>
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14 <param name="in_snp" type="data" format="tabular" label="Input SNP file"/>
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15 </inputs>
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16 <outputs>
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17 <data format_source="in_file" hidden="false" name="default" label="Mutated $in_file.name"/>
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name="in_file" value="seqtk_mutfa.fa"/>
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22 <param name="in_snp" value="seqtk_mutfa.snp"/>
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23 <output name="default" file="seqtk_mutfa.out" ftype="fasta"/>
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24 </test>
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25 </tests>
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26 <help><![CDATA[
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27 **What it does**
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28
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29 the SNP inputs consist of 4 columns: chromosome, 1-based-pos, any, base-changed-to.
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30
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31 ::
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32
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33 # Input fasta
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34 >test0
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35 ACTGACTGAA
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36
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37 # Input SNP file
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38 test0 1 . G
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39 test0 4 . A
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40
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41 This will effect the desired mutations in the output file
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42
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43 ::
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44
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45 # Output result
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46 >test0
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47 GCTAACTGAA
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48
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49 @ATTRIBUTION@
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50 ]]></help>
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51 </tool>
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