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annotate dereplication.xml @ 5:b3c7199d8786 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
author iuc
date Fri, 07 Sep 2018 11:31:31 -0400
parents 4258854759ba
children
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4258854759ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 29f6e6424a37947adbe1eba92f0e7d3c83efc042-dirty
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1 <tool id="vsearch_dereplication" name="VSearch dereplication" 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[
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11 vsearch
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12 @GENERAL@
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13 --derep_fulllength "$infile"
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14 #if str($maxuniquesize):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
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15 --maxuniquesize "$maxuniquesize"
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16 #end if
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17 #if str($minuniquesize):
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
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18 --minuniquesize "$minuniquesize"
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19 #end if
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20 --output "$outfile"
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21 $sizein
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22 $sizeout
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
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23 --strand "$strand"
f29e21388219 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
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24 #if str($topn):
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25 --topn "$topn"
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26 #end if
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27 #if $uc:
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28 --uc "$uc_outfile"
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29 #end if
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30 ]]>
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31 </command>
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32 <inputs>
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33 <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--derep_fulllength)" />
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34 <expand macro="topn" />
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35 <expand macro="sizein" />
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36 <expand macro="sizeout" />
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37 <expand macro="strand" />
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38 <expand macro="uclust_like_output" />
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39 <param name="minuniquesize" type="integer" value="" optional="True" label="Minimum abundance"
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40 help="(--minuniquesize)"/>
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41 <param name="maxuniquesize" type="integer" value="" optional="True" label="Maximum abundance"
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42 help="(--maxuniquesize)"/>
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43 </inputs>
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44 <outputs>
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45 <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" />
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46 <data name="uc_outfile" format="fasta" label="${tool.name} on ${on_string}: UCLUST like output">
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47 <filter>uc is True</filter>
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48 </data>
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49 </outputs>
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50 <tests>
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51 <test>
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52 <param name="infile" value="AF091148_first_rep.fsa.bz2" ftype="fasta" />
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53 <param name="strand" value="both" />
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54 <param name="minuniquesize" value="1" />
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55 <param name="maxuniquesize" value="100000" />
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56 <param name="topn" value="10000" />
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57 <output name="outfile" file="dereplication_result1.fasta" ftype="fasta" />
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58 </test>
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59 <test>
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60 <param name="infile" value="AF091148_first_rep.fsa.bz2" ftype="fasta" />
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61 <param name="strand" value="both" />
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62 <param name="minuniquesize" value="1" />
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63 <param name="maxuniquesize" value="100000" />
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64 <param name="sizeout" value="--sizeout"/>
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65 <param name="topn" value="" />
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66 <output name="outfile" file="dereplication_result2.fasta" ftype="fasta" />
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67 </test>
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68 <test>
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69 <param name="infile" value="AF091148_first_rep.fsa.bz2" ftype="fasta" />
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70 <param name="strand" value="both" />
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71 <param name="minuniquesize" value="1" />
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72 <param name="maxuniquesize" value="100000" />
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73 <param name="sizeout" value="--sizeout"/>
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74 <param name="topn" value="10000" />
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75 <param name="uc" value="--uc" />
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76 <output name="outfile" file="dereplication_result2.fasta" ftype="fasta" />
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77 <output name="uc_outfile" file="dereplication_uc_result3.fasta" ftype="fasta" />
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78 </test>
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79 </tests>
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80 <help>
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81 <![CDATA[
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82 **What it does**
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83
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84 Merge strictly identical sequences contained in filename. Identical sequences are
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85 defined as having the same length and the same string of nucleotides (case insensitive,
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86 T and U are considered the same).
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87
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88 Dereplication options
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89 --derep_fulllength FILENAME dereplicate sequences in the given FASTA file
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90 --maxuniquesize INT maximum abundance for output from dereplication
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91 --minuniquesize INT minimum abundance for output from dereplication
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92 --output FILENAME output FASTA file
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93 --sizein read abundance annotation from input
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94 --sizeout write abundance annotation to output
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95 --strand dereplicate "plus" or "both" strands (plus)
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96 --topn INT output just the n most abundant sequences
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97 --uc FILENAME filename for UCLUST-like output
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98
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99
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100 @EXTERNAL_DOCUMENTATION@
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101
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102
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103 ]]>
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104 </help>
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105 <expand macro="citations" />
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106 </tool>