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annotate seqtk_mutfa.xml @ 15:16f2535c08bf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
author iuc
date Mon, 05 Jun 2017 13:26:30 -0400
parents 55e75a28fde7
children 48a51c72f5e7
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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"/>
16f2535c08bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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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 > '$default'
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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 </tests>
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29 <help><![CDATA[
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30 **What it does**
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31
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32 the SNP inputs consist of 4 columns: chromosome, 1-based-pos, any, base-changed-to.
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33
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34 ::
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35
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36 # Input fasta
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37 >test0
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38 ACTGACTGAA
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39
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40 # Input SNP file
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41 test0 1 . G
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42 test0 4 . A
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43
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44 This will effect the desired mutations in the output file
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45
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46 ::
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47
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48 # Output result
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49 >test0
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50 GCTAACTGAA
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51
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52 @ATTRIBUTION@
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53 ]]></help>
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54 <expand macro="citation" />
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55 </tool>