Mercurial > repos > sanbi-uwc > mothur_test

annotate tools/mothur/cluster.split.xml @ 0:ee4fee239fe7 draft default tip

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planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
author sanbi-uwc
date Fri, 03 Jun 2016 09:32:47 -0400
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1 <tool profile="16.07" id="mothur_cluster_split" name="Cluster.split" version="@WRAPPER_VERSION@.0">
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2 <description>Assign sequences to OTUs (Operational Taxonomic Unit) splits large matrices</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="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 echo 'cluster.split(
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10 splitmethod=$splitby.splitmethod,
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11 #if $splitby.splitmethod == "distance":
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12 #if $splitby.matrix.format == "column":
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13 column=$splitby.matrix.dist,
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14 name=$splitby.matrix.name,
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15 #elif $splitby.matrix.format == "phylip":
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16 phylip=$splitby.matrix.dist,
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17 #if $splitby.matrix.name:
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18 name=$splitby.matrix.name,
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19 #end if
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20 #end if
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21 #elif $splitby.splitmethod == "classify":
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22 column=$splitby.dist,
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23 name=$splitby.name,
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24 taxonomy=$splitby.taxonomy,
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25 #if $splitby.taxlevel > 1:
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26 taxlevel=$splitby.taxlevel,
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27 #end if
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28 #elif $splitby.splitmethod == "fasta":
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29 fasta=$splitby.fasta,
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30 name=$splitby.name,
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31 taxonomy=$splitby.taxonomy,
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32 #if $splitby.taxlevel > 1:
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33 taxlevel=$splitby.taxlevel,
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34 #end if
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35 classic=$splitby.classic,
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36 #end if
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37 #if $count:
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38 count=$count,
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39 #end if
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40 #if $method:
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41 method=$method,
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42 #end if
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43 #if float($cutoff) > 0.0:
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44 cutoff=$cutoff,
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45 #end if
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46 hard=$hard,
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47 #if $precision
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48 precision=$precision,
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49 #end if
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50 large=$large,
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51 cluster=$cluster,
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52 processors='\${GALAXY_SLOTS:-8}'
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53 )'
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54 | sed 's/ //g' ## mothur trips over whitespace
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55 | mothur &&
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56
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57 ## move output files to correct destination
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58 #if $splitby.splitmethod == 'distance':
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59 prefix='$splitby.matrix.dist' &&
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60 #elif $splitby.splitmethod == 'classify':
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61 prefix='$splitby.dist' &&
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62 #elif $splitby.splitmethod == 'fasta':
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63 prefix='$splitby.fasta' &&
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64 #end if
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65 #if $cluster:
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66 mv \${prefix%.dat}*.rabund '$rabund' &&
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67 mv \${prefix%.dat}*.sabund '$sabund' &&
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68 mv \${prefix%.dat}*.list '$otulist' &&
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69 #else:
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70 mv \${prefix%.dat}*.temp . &&
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71 mv \${prefix%.dat}*.file '$splitfile' &&
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72 cat $splitfile &&
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73 #end if
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74 mv mothur.*.logfile '$logfile'
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75 ]]></command>
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76 <inputs>
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77 <conditional name="splitby">
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78 <param name="splitmethod" type="select" label="Split by" help="">
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79 <option value="distance">Distance</option>
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80 <option value="classify">Classification</option>
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81 <option value="fasta">Classification using fasta</option>
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82 </param>
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83 <when value="distance">
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84 <conditional name="matrix">
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85 <param name="format" type="select" label="Select a Distance Matrix Format" help="">
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86 <option value="column">Pairwise Column Matrix</option>
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87 <option value="phylip">Phylip Distance Matrix</option>
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88 </param>
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89 <when value="column">
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90 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
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91 <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
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92 </when>
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93 <when value="phylip">
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94 <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
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95 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
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96 </when>
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97 </conditional>
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98 </when>
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99 <when value="classify">
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100 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
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101 <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
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102 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy (from Classify.seqs)"/>
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103 <param name="taxlevel" type="integer" value="1" label="taxlevel - taxonomy level for split (default=1)" help="taxonomy level you want to use to split the distance file, default=1, meaning use the first taxon in each list"/>
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104 </when>
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105 <when value="fasta">
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106 <param name="fasta" type="data" format="mothur.align" label="fasta - Aligned Sequences" help="must be aligned sequences (mothur.align)"/>
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107 <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
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108 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy (from Classify.seqs)"/>
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109 <param name="taxlevel" type="integer" value="3" label="taxlevel - taxonomy level for split (default=3)" help="taxonomy level you want to use to split the distance file, default=1, meaning use the first taxon in each list"/>
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110 <param name="classic" type="boolean" checked="false" truevalue="true" falsevalue="false" label="classic - Use cluster.classic"/>
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111 </when>
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112 </conditional>
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113 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
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114 <param name="method" type="select" label="method - Select a Clustering Method" help="">
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115 <option value="furthest">Furthest neighbor</option>
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116 <option value="nearest">Nearest neighbor</option>
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117 <option value="average" selected="true">Average neighbor</option>
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118 </param>
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119 <param name="cutoff" type="float" value="0.0" min="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0" help="Ignore pairwise distances larger than this, a common value would be 0.25"/>
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120 <param name="hard" type="boolean" checked="true" truevalue="true" falsevalue="false" label="hard - Use hard cutoff instead of rounding" help=""/>
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121 <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values" help="Set higher precision for longer genome scale sequence lengths">
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122 <option value="10">.1</option>
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123 <option value="100" selected="true">.01</option>
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124 <option value="1000">.001</option>
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125 <option value="10000">.0001</option>
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126 <option value="100000">.00001</option>
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127 <option value="1000000">.000001</option>
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128 </param>
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129 <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - distance matrix is too large to fit in RAM" help="If your job fails due to not enough memory error, set this to true to rerun"/>
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130 <param name="cluster" type="boolean" falsevalue="false" truevalue="true" checked="true" label="The cluster parameter allows you to indicate whether you want to run the clustering or just split the distance matrix, default=T"/>
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131 </inputs>
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132 <outputs>
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133 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
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134 <data name="rabund" format="mothur.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
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135 <data name="sabund" format="mothur.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
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136 <data name="otulist" format="mothur.list" label="${tool.name} on ${on_string}: list (OTU List)"/>
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137 <collection name="splitdist" type="list" label="${tool.name} on ${on_string}: split dist">
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138 <filter>not cluster</filter>
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139 <discover_datasets pattern=".*?\.dist\.(?P&lt;designation&gt;.*)\.temp" format="mothur.dist"/>
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140 </collection>
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141 <collection name="splitnames" type="list" label="${tool.name} on ${on_string}: split names">
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142 <filter>not cluster</filter>
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143 <discover_datasets pattern=".*?\.names\.(?P&lt;designation&gt;.*)\.temp" format="mothur.names"/>
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144 </collection>
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145 <data name="splitfile" format="txt" label="${tool.name} on ${on_string}: split.file">
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146 <filter>not cluster</filter>
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147 </data>
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148 </outputs>
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149 <tests>
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150 <test><!-- test with distance method -->
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151 <param name="splitmethod" value="distance"/>
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152 <param name="format" value="phylip"/>
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153 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
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154 <output name="otulist" md5="2613ef0a1805ba9de012a41e938d8947" ftype="mothur.list"/>
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155 <output name="rabund" md5="4df813ec2d51c373a846a82380c7a1f8" ftype="mothur.rabund"/>
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156 <output name="sabund" md5="8d6813a5e8d2ad426a0ee5fdd99f1a19" ftype="mothur.sabund"/>
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157 <expand macro="logfile-test"/>
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158 </test>
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159 <test><!-- test with cluster false -->
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160 <param name="splitmethod" value="distance"/>
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161 <param name="format" value="phylip"/>
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162 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
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163 <param name="cluster" value="false"/>
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164 <output name="splitfile" ftype="txt">
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165 <assert_contents>
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166 <has_text text="column"/>
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167 <has_text text="dist"/>
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168 <has_text text="names"/>
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169 <has_text text="temp"/>
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170 </assert_contents>
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171 </output>
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172 <output_collection name="splitnames" count="4">
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173 <element name="0" md5="27037eeb3e696888b24653d0996261cd" ftype="mothur.names"/>
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174 </output_collection>
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175 <output_collection name="splitdist" count="3">
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176 <element name="4" md5="f751aee00b598d3b6691d34f67dbc8d5" ftype="mothur.dist"/>
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177 </output_collection>
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178 <expand macro="logfile-test"/>
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179 </test>
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180 <test><!-- test with classify method -->
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181 <param name="splitmethod" value="classify"/>
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182 <param name="format" value="column"/>
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183 <param name="dist" value="amazon.pair.dist" ftype="mothur.pair.dist"/>
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184 <param name="name" value="amazon.names" ftype="mothur.names"/>
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185 <param name="taxonomy" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
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186 <output name="otulist" md5="d6eba624ad79759c530b9bc3285a1361" ftype="mothur.list"/>
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187 <output name="rabund" md5="2a165e1e40644fccb8cc9f53d8915bc3" ftype="mothur.rabund"/>
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188 <output name="sabund" md5="7aad8a9ca0eade414d6eba1f8bef960f" ftype="mothur.sabund"/>
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189 <expand macro="logfile-test"/>
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190 </test>
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191 <test><!-- test with fasta -->
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192 <param name="splitmethod" value="fasta"/>
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193 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
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194 <param name="name" value="amazon.align_head.names" ftype="mothur.names"/>
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195 <param name="taxonomy" value="amazon.align_head.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
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196 <param name="cutoff" value="9999"/>
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197 <output name="otulist" md5="a1279248cf2bc1094e0046b2cff1b785" ftype="mothur.list"/>
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198 <output name="rabund" md5="65ec9f326cd92fc607679b9902ec8430" ftype="mothur.rabund"/>
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199 <output name="sabund" md5="854d3acd15f64299c5d9d9e18f2d51b4" ftype="mothur.sabund"/>
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200 <expand macro="logfile-test"/>
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201 </test>
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202 </tests>
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203 <help>
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204 <![CDATA[
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205
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206 @MOTHUR_OVERVIEW@
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207
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208
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209 **Command Documenation**
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210
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211 The cluster.split_ command assign sequences to OTUs (Operational Taxonomy Unit).
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212
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213 .. _cluster.split: http://www.mothur.org/wiki/Cluster.split
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214
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215 v1.28.0: Upgraded to Mothur 1.33, introduced cluster boolean.
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216
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217 ]]>
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218 </help>
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219 <expand macro="citations"/>
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220 </tool>