Mercurial > repos > iuc > vsearch

annotate masking.xml @ 0:24e4f42410e5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
author iuc
date Mon, 11 May 2015 22:46:54 -0400
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0
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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1 <tool id="vsearch_masking" name="VSearch masking" version="@VERSION@.0">
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2 <description></description>
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3 <macros>
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4 <import>vsearch_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <expand macro="version_command" />
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9 <command>
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10 <![CDATA[
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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11 vsearch
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12 @GENERAL@
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13 #if $qmask != 'no':
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14 --qmask $qmask
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15 #end if
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16 $hardmask
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17 --maskfasta "$infile"
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18 --output $outfile
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19
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20 ]]>
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21 </command>
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22 <inputs>
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23 <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--maskfasta)" />
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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24 <expand macro="qmask" />
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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25 <expand macro="hardmask" />
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26 </inputs>
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27 <outputs>
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28 <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" />
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="infile" value="db.fasta" ftype="fasta" />
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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33 <param name="qmask" value="dust"/>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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34 <param name="hardmask" value="True"/>
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35 <output name="outfile" file="masking_result1.fasta" ftype="fasta" />
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36 </test>
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37 <test>
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38 <param name="infile" value="db.fasta" ftype="fasta" />
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39 <param name="qmask" value="soft"/>
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40 <param name="hardmask" value="True"/>
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41 <output name="outfile" file="masking_result2.fasta" ftype="fasta" />
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42 </test>
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43 </tests>
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44 <help>
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45 <![CDATA[
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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46 **What it does**
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47
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48 An input sequence can be composed of lower- or uppercase nucleotides. Lowercase nucleotides
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49 are silently set to uppercase before masking, unless the −−qmask soft option is used.
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50 Here are the results of combined masking options −−qmask (or −−dbmask for database sequences) and −−hardmask, assuming each input sequences contains both lower and uppercase nucleotides:
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51
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52 ===== ======== ================================================
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53 qmask hardmask action
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54 ===== ======== ================================================
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55 none off no masking, all symbols uppercased
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56 none on no masking, all symbols uppercased
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57 dust off masked symbols lowercased, others uppercased
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58 dust on masked symbols changed to Ns, others uppercased
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59 soft off lowercase symbols masked, no case changes
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60 soft on lowercase symbols masked and changed to Ns
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61 ===== ======== ================================================
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62
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63 Masking options
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64 --hardmask mask by replacing with N instead of lower case
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65 --maskfasta FILENAME mask sequences in the given FASTA file
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66 --output FILENAME output to specified FASTA file
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67 --qmask mask seqs with "dust", "soft" or "none" method (dust)
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68
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69 @EXTERNAL_DOCUMENTATION@
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70
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71 -------
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72
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73 @REFERENCES@
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74
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75
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76 ]]>
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77 </help>
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78 <expand macro="citations" />
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79 </tool>