Mercurial > repos > iuc > mothur_cluster

annotate cluster.xml @ 2:6f2cdccbfa48 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:08:08 -0400
parents 8c1b609f566d
children 3bb756df109c
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8c1b609f566d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_cluster" name="Cluster" version="@WRAPPER_VERSION@.0">
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2 <description>Assign sequences to OTUs (Operational Taxonomic Unit)</description>
8c1b609f566d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
2
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6 <expand macro="requirements">
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7 <requirement type="package" version="2.6.0">vsearch</requirement>
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8 </expand>
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9 <expand macro="stdio"/>
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10 <expand macro="version_command"/>
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11 <command><![CDATA[
2
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12 @SHELL_OPTIONS@
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13
2
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14 ## create symlinks to input datasets
6f2cdccbfa48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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15 ln -s '$matrix.dist' matrix.dist.dat &&
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16 ln -s '$matrix.name' matrix.name.dat &&
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17 ln -s '$count' count.dat &&
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18
2
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19 echo 'cluster(
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20 #if $matrix.format == "phylip":
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21 phylip=matrix.dist.dat,
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22 #else
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23 column=matrix.dist.dat,
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24 #end if
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25 #if $matrix.name:
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26 name=matrix.name.dat,
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27 #end if
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28 #if $count:
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29 count=count.dat,
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30 #end if
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31 #if float($cutoff) > 0.0:
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32 cutoff=$cutoff,
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33 #end if
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34 #if $select_method.method =="opti":
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35 metric=$select_method.metric,
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36 initialize=$select_method.initialize,
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37 delta=$select_method.delta,
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38 iters=$select_method.iters,
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39 #end if
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40 precision=$precision,
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41 sim=$sim,
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42 method=$select_method.method
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43 )'
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44 | sed 's/ //g' ## mothur trips over whitespace
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45 | mothur
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46 | tee mothur.out.log
0
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47 ]]></command>
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48 <inputs>
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49 <conditional name="matrix">
2
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50 <param name="format" type="select" label="Cluster based on" help="">
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51 <option value="column">Pairwise Column Matrix</option>
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52 <option value="phylip">Phylip Distance Matrix</option>
2
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53 <option value="fasta">Fasta (VSEARCH)</option>
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54 </param>
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55 <when value="column">
2
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56 <param name="dist" argument="column" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
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57 <param argument="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
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58 </when>
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59 <when value="phylip">
2
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60 <param name="dist" argument="phylip" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
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61 <param argument="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
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62 </when>
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63 <when value="fasta">
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64 <param argument="fasta" type="data" format="mothur.align,fasta" label="Fasta file"/>
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65 </when>
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66 </conditional>
2
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67 <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
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68 <conditional name="select_method">
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69 <expand macro="param-clustermethods">
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70 <expand macro="option-vsearch-clustermethods"/>
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71 </expand>
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72 <when value="furthest"/>
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73 <when value="nearest"/>
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74 <when value="average"/>
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75 <when value="agc">
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76 <param argument="fasta" type="data" format="mothur.align,fasta" label="Fasta file"/>
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77 </when>
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78 <when value="dgc">
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79 <param argument="fasta" type="data" format="mothur.align,fasta" label="Fasta file"/>
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80 </when>
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81 <when value="opti">
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82 <expand macro="params-opticlust"/>
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83 </when>
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84 </conditional>
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85 <param argument="cutoff" type="float" value="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0.0"
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86 help="Ignore pairwise distances larger than this, a common value would be 0.10"/>
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87 <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values"
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88 help="Set higher precision for longer genome scale sequence lengths">
0
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89 <option value="10">.1</option>
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90 <option value="100" selected="true">.01</option>
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91 <option value="1000">.001</option>
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92 <option value="10000">.0001</option>
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93 <option value="100000">.00001</option>
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94 <option value="1000000">.000001</option>
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95 </param>
2
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96 <param argument="sim" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sim - Matrix values are Similary instead of Distance"/>
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97 <expand macro="param-savelog"/>
0
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98 </inputs>
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99 <outputs>
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100 <expand macro="logfile-output"/>
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101 <data name="rabund" format="mothur.rabund" from_work_dir="matrix.dist*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
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102 <data name="sabund" format="mothur.sabund" from_work_dir="matrix.dist*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
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103 <data name="otulist" format="mothur.list" from_work_dir="matrix.dist*.list" label="${tool.name} on ${on_string}: list (OTU List)"/>
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104 </outputs>
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105 <tests>
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106 <test><!-- test with phylip input -->
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107 <param name="format" value="phylip"/>
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108 <param name="dist" value="amazon.dist"/>
2
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109 <output name="rabund" ftype="mothur.rabund">
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110 <assert_contents>
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111 <has_line_matching expression="^0\.03(\t\d+)+$"/>
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112 </assert_contents>
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113 </output>
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114 <output name="sabund" ftype="mothur.sabund">
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115 <assert_contents>
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116 <has_line_matching expression="^0\.03(\t\d+)+$"/>
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117 </assert_contents>
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118 </output>
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119 <output name="otulist" ftype="mothur.list">
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120 <assert_contents>
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121 <expand macro="test-list-format"/>
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122 <has_text text="0.03"/>
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123 <has_text text="U68688"/>
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124 </assert_contents>
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125 </output>
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126 <param name="savelog" value="true"/>
0
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127 <expand macro="logfile-test"/>
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128 </test>
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129 <test><!-- test with column input -->
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130 <param name="format" value="column"/>
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131 <param name="dist" value="amazon.pair.dist"/>
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132 <param name="name" value="amazon.names"/>
2
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133 <output name="rabund" ftype="mothur.rabund">
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134 <assert_contents>
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135 <has_line_matching expression="^0\.03(\t\d+)+$"/>
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136 </assert_contents>
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137 </output>
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138 <output name="sabund" ftype="mothur.sabund">
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139 <assert_contents>
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140 <has_line_matching expression="^0\.03(\t\d+)+$"/>
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141 </assert_contents>
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142 </output>
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143 <output name="otulist" ftype="mothur.list">
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144 <assert_contents>
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145 <expand macro="test-list-format"/>
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146 <has_text text="0.03"/>
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147 <has_text text="U68688"/>
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148 </assert_contents>
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149 </output>
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150 <param name="savelog" value="true"/>
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151 <expand macro="logfile-test"/>
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152 </test>
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153 <test><!-- test with column input -->
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154 <param name="format" value="column"/>
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155 <param name="dist" value="amazon.pair.dist"/>
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156 <param name="name" value="amazon.names"/>
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157 <output name="rabund" ftype="mothur.rabund">
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158 <assert_contents>
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159 <has_line_matching expression="^0\.03(\t\d+)+$"/>
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160 </assert_contents>
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161 </output>
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162 <output name="sabund" ftype="mothur.sabund">
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163 <assert_contents>
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164 <has_line_matching expression="^0\.03(\t\d+)+$"/>
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165 </assert_contents>
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166 </output>
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167 <output name="otulist" ftype="mothur.list">
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168 <assert_contents>
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169 <expand macro="test-list-format"/>
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170 <has_text text="0.03"/>
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171 <has_text text="U68688"/>
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172 </assert_contents>
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173 </output>
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174 <param name="savelog" value="true"/>
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175 <expand macro="logfile-test"/>
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176 </test>
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177 </tests>
2
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178 <help><![CDATA[
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179
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180 @MOTHUR_OVERVIEW@
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181
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182 **Command Documentation**
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183
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184 The cluster_ command assign sequences to OTUs (Operational Taxonomy Unit). The assignment is based on a phylip-formatted_distance_matrix_ or a column-formatted_distance_matrix_ and name_ file. It generates a list_, a sabund_ (Species Abundance), and a rabund_ (Relative Abundance) file.
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185
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186 .. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
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187 .. _column-formatted_distance_matrix: https://www.mothur.org/wiki/Column-formatted_distance_matrix
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188 .. _name: https://www.mothur.org/wiki/Name_file
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189 .. _list: https://www.mothur.org/wiki/List_file
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190 .. _rabund: https://www.mothur.org/wiki/Rabund_file
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191 .. _sabund: https://www.mothur.org/wiki/Sabund_file
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192 .. _cluster: https://www.mothur.org/wiki/Cluster
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193
2
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194 ]]></help>
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195 <expand macro="citations"/>
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196 </tool>