Mercurial > repos > iuc > mothur_consensus_seqs

annotate consensus.seqs.xml @ 3:f573fcdeec56 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 283d5933cd945b7815b3da2ce45baa60d73e9746
author iuc
date Fri, 06 Apr 2018 04:02:03 -0400
parents 4f4de4518aca
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1 <tool profile="16.07" id="mothur_consensus_seqs" name="Consensus.seqs" version="@WRAPPER_VERSION@.0">
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2 <description>Find a consensus sequence for each OTU or phylotype</description>
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3 <macros>
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4 <import>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><![CDATA[
2
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10 @SHELL_OPTIONS@
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11
2
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12 ## create symlinks to input datasets
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13 ln -s '$fasta' fasta.dat &&
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14 ln -s '$name' name.dat &&
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15 ln -s '$count' count.dat &&
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16 #if $perotu.use == "yes":
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17 ln -s '$perotu.otu' perotu.otu.dat &&
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18 #end if
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19
2
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20 echo 'consensus.seqs(
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21 fasta=fasta.dat
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22 #if $name:
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23 ,name=name.dat
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24 #end if
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25 #if $cutoff:
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26 ,cutoff=$cutoff
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27 #end if
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28 #if $perotu.use == "yes":
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29 ,list=perotu.otu.dat
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30 #if $perotu.label:
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31 ,label=${ str($perotu.label).replace(",","-") }
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32 #end if
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33 #end if
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34 #if $count:
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35 ,count=count.dat
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36 #end if
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37 )'
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38 | sed 's/ //g' ## mothur trips over whitespace
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39 | mothur
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40 | tee mothur.out.log
0
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41 ]]></command>
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42 <inputs>
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43 <param name="fasta" type="data" format="mothur.align" label="fasta - Sequences to Bin" help="Sequences must be aligned"/>
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44 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
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45 <conditional name="perotu">
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46 <param name="use" type="select" label="Consensus sequence">
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47 <option value="no" selected="true">Single consensus sequence</option>
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48 <option value="yes">Consensus sequence for each OTU in list</option>
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49 </param>
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50 <when value="yes">
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51 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
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52 <param name="label" type="select" optional="true" multiple="true" label="label - Select OTU Labels" help="By default all labels are used">
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53 <expand macro="labeloptions"/>
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54 </param>
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55 </when>
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56 <when value="no"/>
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57 </conditional>
2
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58 <param name="cutoff" type="integer" value="" optional="True" min="1" max="100" label="Cutoff - set a percentage of sequences that support the base"
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59 help="For example: cutoff=95 would return the base that was supported by at least 95% of sequences. Must be between 1 and 100. Optional"/>
0
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60 <param name="count" type="data" format="mothur.count_table" optional="true" label="Count - a count table" help="this file can be generated by count.seqs"/>
2
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61 <expand macro="param-savelog"/>
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62 </inputs>
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63 <outputs>
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64 <expand macro="logfile-output"/>
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65 <data name="summary" format="tabular" from_work_dir="fasta*.cons.summary" label="${tool.name} on ${on_string}: cons.summary">
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66 <filter>perotu['use'] == 'no'</filter>
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67 </data>
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68 <data name="cons_fasta" format="mothur.align" from_work_dir="fasta*.cons.fasta" label="${tool.name} on ${on_string}: cons.fasta">
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69 <filter>perotu['use'] == 'no'</filter>
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70 </data>
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71 <collection name="consensusfastas" type="list" label="${tool.name} on ${on_string}: consensus fasta files per OTU">
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72 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.cons\.fasta" format="mothur.align"/>
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73 <filter>perotu['use'] == 'yes'</filter>
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74 </collection>
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75 <collection name="consensusnames" type="list" label="${tool.name} on ${on_string}: consensus names files per OTU">
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76 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.cons\.names" format="mothur.names"/>
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77 <filter>perotu['use'] == 'yes'</filter>
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78 </collection>
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79 <collection name="consensussummaries" type="list" label="${tool.name} on ${on_string}: consensus summary files per OTU">
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80 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.cons\.summary" format="tabular"/>
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81 <filter>perotu['use'] == 'yes'</filter>
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82 </collection>
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83 </outputs>
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84 <tests>
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85 <test><!-- test with default values -->
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86 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
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87 <output name="summary" md5="61a0e170a8b881135421afd0cea8305a" ftype="tabular"/>
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88 <output name="cons_fasta" md5="82f3475b61f240eba09597a409364c04" ftype="mothur.align"/>
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89 <param name="savelog" value="true"/>
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90 <expand macro="logfile-test"/>
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91 </test>
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92 <test><!-- test with list file -->
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93 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
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94 <param name="use" value="yes"/>
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95 <param name="otu" value="amazon.align_head.list" ftype="mothur.list"/>
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96 <param name="count" value="amazon.align_head.count_table" ftype="mothur.count_table"/>
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97 <param name="labels" value="unique,0.30,0.33"/>
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98 <output_collection name="consensusfastas" count="3">
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99 <element name="0.30" md5="a5c8c17814f02124194dba2e37f566c7" ftype="mothur.align"/>
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100 </output_collection>
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101 <output_collection name="consensusnames" count="3">
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102 <element name="0.30" md5="9de4f7e774e0c16eaf7cf6ffbba9d475" ftype="mothur.names"/>
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103 </output_collection>
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104 <output_collection name="consensussummaries" count="3">
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105 <element name="0.30" md5="d595234c6018dfcc1465e59d35d59205" ftype="tabular"/>
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106 </output_collection>
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107 <param name="savelog" value="true"/>
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108 <expand macro="logfile-test"/>
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109 </test>
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110 </tests>
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111 <help><![CDATA[
0
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112
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113 @MOTHUR_OVERVIEW@
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114
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115 **Command Documentation**
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116
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117 The consensus.seqs_ command can be used in 2 ways: create a consensus sequence from a fastafile, or with a listfile create a consensus sequence for each otu. Sequences must be aligned.
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118
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119 .. _consensus.seqs: https://www.mothur.org/wiki/Consensus.seqs
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120
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121 ]]></help>
0
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122 <expand macro="citations"/>
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123 </tool>