Mercurial > repos > iuc > mothur_get_oturep

annotate get.oturep.xml @ 0:d568050a95be draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:33:26 -0400
parents
children 17b63c3cc04d
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d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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1 <tool profile="16.07" id="mothur_get_oturep" name="Get.oturep" version="@WRAPPER_VERSION@.0">
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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2 <description>Generate a fasta with a representative sequence for each OTU</description>
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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3 <macros>
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4 <import>macros.xml</import>
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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5 </macros>
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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6 <expand macro="requirements"/>
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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7 <expand macro="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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9 ## create symlinks to input datasets
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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10 ln -s "$otu" otu.dat &&
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11 ln -s "$fasta" fasta.dat &&
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 ln -s "$input.dist" input.dist.dat &&
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 ln -s "$input.name" input.name.dat &&
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14 ln -s "$count" count.dat &&
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15 #if $pick.type == "yes":
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16 ln -s "$pick.group" pick.group.dat &&
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17 #end if
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18
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19 echo 'get.oturep(
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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20 list=otu.dat,
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 #if $fasta:
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22 fasta=fasta.dat,
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 #end if
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24 #if $input.source == "column":
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25 column=input.dist.dat,
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 name=input.name.dat,
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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27 #elif $input.source == "phylip":
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28 phylip=input.dist.dat,
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 #if $input.name:
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30 name=input.name.dat,
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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31 #end if
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32 #end if
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 #if $label:
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34 label=${ str($label).replace(",","-") },
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 #end if
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 #if $pick.type == "yes":
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 #if $pick.group:
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 group=pick.group.dat,
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 #end if
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 #if $pick.groups:
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 groups=${ str($pick.groups).replace(",","-") },
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 #end if
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 #end if
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44 #if $sorted:
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45 sorted=$sorted,
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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46 #end if
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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47 #if $count and not $input.name:
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48 count=count.dat,
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49 #end if
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50 method=$method,
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51 large=$large
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52 )'
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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53 | sed 's/ //g' ## mothur trips over whitespace
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54 | mothur
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55 ]]></command>
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56 <inputs>
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57 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
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58 <conditional name="input">
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59 <param name="source" type="select" label="Distance Matrix Format">
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60 <option value="column">Pairwise Column Distance Matrix</option>
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61 <option value="phylip">Phylip Distance Matrix</option>
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62 </param>
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63 <when value="column">
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64 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
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65 <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
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66 </when>
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67 <when value="phylip">
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68 <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
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69 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names"/>
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70 </when>
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71 </conditional>
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72 <param name="fasta" type="data" format="fasta" optional="true" label="fasta - Fasta"/>
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73 <conditional name="pick">
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74 <param name="type" type="select" label="Parse a group file into abundant and rare groups?" help="">
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75 <option value="no" selected="true">No</option>
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76 <option value="yes">Yes</option>
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77 </param>
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78 <when value="no"/>
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79 <when value="yes">
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80 <param name="group" type="data" format="mothur.groups" label="group - Group file for the OTU List"/>
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81 <param name="groups" type="select" multiple="true" label="groups - Group Selection (all used if none are selected)">
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82 <options>
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83 <filter type="data_meta" ref="group" key="groups"/>
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84 </options>
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85 </param>
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86 </when>
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87 </conditional>
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88 <param name="label" type="select" multiple="true" label="label - OTU Labels">
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89 <expand macro="labeloptions"/>
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90 </param>
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91 <param name="sorted" type="select" label="sorted - Sort Sequences by">
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92 <option value="">Don't sort</option>
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93 <option value="name">Sequence Name</option>
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94 <option value="number">Bin Number</option>
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95 <option value="size">Bin Size</option>
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96 <option value="group">Group</option>
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97 </param>
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98 <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Distance Matrix is very Large"/>
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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99 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count table" help="Cannot supply both a names and count table. Will be ignored if you also supplied a name file. Generated by count.seqs"/>
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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100 <param name="method" type="select" label="method - select the method of selecting the representative sequence" help="the distance method finds the sequence with the smallest maximum distance to other sequences. The abundance method chooses the abundant sequence in the OTU as the representative. Default=distance">
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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101 <option value="distance" selected="true">distance</option>
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102 <option value="abundance">abundance</option>
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103 </param>
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104 </inputs>
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105 <outputs>
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106 <expand macro="logfile-output"/>
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107 <collection name="names_out" type="list" label="${tool.name} on ${on_string}: rep.names">
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108 <filter>input['name'] or not count</filter>
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109 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rep\.names" format="mothur.names"/>
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110 </collection>
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111 <collection name="fasta_out" type="list" label="${tool.name} on ${on_string}: rep.fasta">
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112 <filter>fasta</filter>
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113 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rep\.fasta" format="fasta"/>
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114 </collection>
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115 <collection name="count_out" type="list" label="${tool.name} on ${on_string}: rep.count_table">
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116 <filter>count and not input['name']</filter>
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117 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rep\.count_table" format="mothur.count_table"/>
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118 </collection>
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119 </outputs>
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120 <tests>
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121 <test><!-- test with phylip -->
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122 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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123 <param name="source" value="phylip"/>
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124 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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125 <param name="name" value="amazon1.names" ftype="mothur.names"/>
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126 <output_collection name="names_out" count="36">
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127 <element name="0.27" md5="39ff2858909d49633871d5a625585de5" ftype="mothur.names"/>
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128 </output_collection>
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129 <expand macro="logfile-test"/>
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130 </test>
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131 <test><!-- test with column and label select -->
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132 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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133 <param name="source" value="column"/>
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134 <param name="dist" value="amazon.pair.dist" ftype="mothur.pair.dist"/>
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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135 <param name="name" value="amazon1.names" ftype="mothur.names"/>
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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136 <param name="label" value="unique,0.05,0.27,0.45"/>
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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137 <output_collection name="names_out" count="4">
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138 <element name="0.27" md5="be6dccdd3d4619c3ac465246c826209a" ftype="mothur.names"/>
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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139 </output_collection>
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140 <expand macro="logfile-test"/>
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141 </test>
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142 <test><!-- test with fasta and sorting-->
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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143 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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144 <param name="source" value="phylip"/>
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145 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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146 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
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147 <param name="label" value="0.05,0.27"/>
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148 <param name="sorted" value="name"/>
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149 <output_collection name="names_out" count="2">
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150 <element name="0.27" md5="39ff2858909d49633871d5a625585de5" ftype="mothur.names"/>
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151 </output_collection>
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152 <output_collection name="fasta_out" count="2">
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153 <element name="0.27" md5="a9d9622b6f5fcbe8acdc05df5484ffc4" ftype="fasta"/>
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154 </output_collection>
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155 <expand macro="logfile-test"/>
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156 </test>
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157 <test><!-- test with group file -->
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158 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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159 <param name="source" value="column"/>
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160 <param name="dist" value="amazon.pair.dist" ftype="mothur.pair.dist"/>
d568050a95be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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161 <param name="name" value="amazon1.names" ftype="mothur.names"/>
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162 <param name="label" value="unique,0.05,0.27,0.45"/>
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163 <param name="type" value="yes"/>
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164 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
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165 <param name="groups" value="forest,pasture"/>
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166 <param name="count" value="amazon1.count_table" ftype="mothur.count_table"/> <!-- should be ignored as we also supplied name file -->
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167 <output_collection name="names_out" count="8">
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168 <element name="0.27.pasture" md5="34f87d93fd9ebbefed9754f627f502fd" ftype="mothur.names"/>
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169 </output_collection>
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170 <expand macro="logfile-test"/>
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171 </test>
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172 <test><!-- test with count table -->
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173 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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174 <param name="source" value="phylip"/>
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175 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
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176 <param name="label" value="unique,0.05,0.27"/>
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177 <param name="count" value="amazon1.count_table" ftype="mothur.count_table"/>
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178 <output_collection name="count_out" count="3">
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179 <element name="0.27" md5="6b1afd712825af4bf8cb4ab8304df903" ftype="mothur.count_table"/>
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180 </output_collection>
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181 <expand macro="logfile-test"/>
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182 </test>
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183 </tests>
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184 <help>
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185 <![CDATA[
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186
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187 @MOTHUR_OVERVIEW@
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188
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189
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190 **Command Documenation**
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191
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192 The get.oturep_ command generates a fasta-formatted sequence file containing only a representative sequence for each OTU. The opposite of the bin.seqs command.
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193
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194 .. _get.oturep: http://www.mothur.org/wiki/Get.oturep
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195
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196 v1.23.0: Updated to Mothur 1.33, added count and method parameter
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197 ]]>
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198 </help>
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199 <expand macro="citations"/>
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200 </tool>