Mercurial > repos > sanbi-uwc > mothur_test

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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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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <tool profile="16.07" id="mothur_tree_shared" name="Tree.shared" version="@WRAPPER_VERSION@.0">
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2 <description>Generate a newick tree for dissimilarity among groups</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 'tree.shared(
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10 #if $input.source == "shared":
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11 shared=$input.dist,
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12 #if $input.groups:
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13 groups=${ str($input.groups).replace(",","-") },
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14 #end if
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15 #if $input.label:
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16 label=${ str($input.label).replace(",","-") },
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17 #end if
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18 #if $input.subsampling.use == "yes":
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19 #if $input.subsampling.subsample:
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20 subsample=$input.subsampling.subsample,
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21 #else
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22 subsample=T,
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23 #end if
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24 #if $input.subsampling.iters:
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25 iters="$input.subsampling.iters,
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26 #end if
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27 #end if
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28 #elif $input.source == "column":
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29 column=$input.dist,
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30 name=$input.name,
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31 #elif $input.source == "phylip":
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32 phylip=$input.dist,
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33 #if $input.name:
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34 name=$input.name,
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35 #end if
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36 #else
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37 count=$input.name,
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38 #end if
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39 #if $calc:
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40 calc=${ str($calc).replace(",","-") },
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41 #end if
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42 processors='\${GALAXY_SLOTS:-8}'
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43 )'
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44 | sed 's/ //g' ## mothur trips over whitespace
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45 | mothur &&
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46
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47 ## move output files to correct destination
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48 prefix='$input.dist' &&
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49 #if $input.source == 'shared':
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50 mv \${prefix%.dat}*.tre . &&
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51 #else
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52 mv \${prefix%.dat}*.tre '$tre' &&
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53 #end if
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54 mv mothur.*.logfile '$logfile'
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55 ]]></command>
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56 <inputs>
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57 <conditional name="input">
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58 <param name="source" type="select" label="Select input format">
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59 <option value="shared">OTU Shared</option>
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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 <option value="count">Count file</option>
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63 </param>
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64 <when value="column">
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65 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
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66 <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
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67 </when>
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68 <when value="phylip">
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69 <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
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70 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names"/>
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71 </when>
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72 <when value="shared">
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73 <param name="dist" type="data" format="mothur.shared" label="shared - OTU Shared"/>
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74 <param name="label" type="select" label="label - OTU Labels" multiple="true">
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75 <options>
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76 <filter type="data_meta" ref="dist" key="labels"/>
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77 </options>
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78 </param>
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79 <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
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80 <options>
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81 <filter type="data_meta" ref="dist" key="groups"/>
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82 </options>
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83 </param>
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84 <conditional name="subsampling">
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85 <param name="use" type="select" label="subsample">
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86 <option value="no" selected="true">no</option>
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87 <option value="yes">yes</option>
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88 </param>
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89 <when value="yes">
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90 <param name="subsample" type="integer" value="" min="0" optional="true" label="subsample (defaults to the size of the smallest group)" help="Should not exceed the number of sequences in any group"/>
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91 <param name="iters" type="integer" value="" min="1" optional="true" label="iters - Number of iterations to try (default 1000)"/>
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92 </when>
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93 <when value="no"/>
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94 </conditional>
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95 </when>
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96 <when value="count">
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97 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
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98 <param name="name" type="data" format="mothur.count_table" label="count - count_table file"/>
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99 </when>
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100 </conditional>
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101 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
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102 <option value="sharedsobs">sharedsobs - Shared community richness the observed richness shared between two or more samples</option>
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103 <option value="sharedchao">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option>
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104 <option value="sharedace">sharedace - Shared community richness the two sample shared ACE richness estimator</option>
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105 <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option>
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106 <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
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107 <option value="jest">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option>
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108 <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option>
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109 <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option>
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110 <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option>
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111 <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option>
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112 <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option>
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113 <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
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114 <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option>
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115 <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>
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116 <option value="hamming">hamming - Community Membership Similarity -</option>
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117 <option value="memchi2">memchi2 - Community Membership Similarity -</option>
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118 <option value="memchord">memchord - Community Membership Similarity -</option>
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119 <option value="memeuclidean">memeuclidean - Community Membership Similarity -</option>
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120 <option value="mempearson">mempearson - Community Membership Similarity -</option>
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121 <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
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122 <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
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123 <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
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124 <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
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125 <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
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126 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
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127 <option value="canberra">canberra - Community Structure Similarity -</option>
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128 <option value="gower">gower - Community Structure Similarity -</option>
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129 <option value="hellinger">hellinger - Community Structure Similarity -</option>
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130 <option value="manhattan">manhattan - Community Structure Similarity -</option>
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131 <option value="odum">odum - Community Structure Similarity -</option>
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132 <option value="soergel">soergel - Community Structure Similarity -</option>
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133 <option value="spearman">spearman - Community Structure Similarity -</option>
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134 <option value="speciesprofile">speciesprofile - Community Structure Similarity -</option>
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135 <option value="structchi2">structchi2 - Community Structure Similarity -</option>
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136 <option value="structchord">structchord - Community Structure Similarity -</option>
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137 <option value="structeuclidean">structeuclidean - Community Structure Similarity -</option>
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138 <option value="structkulczynski">structkulczynski - Community Structure Similarity -</option>
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139 <option value="structpearson">structpearson - Community Structure Similarity -</option>
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140 <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option>
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141 <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option>
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142 </param>
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143 </inputs>
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144 <outputs>
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145 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
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146 <data name="tre" format="mothur.tre" label="${tool.name} on ${on_string}: tre">
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147 <filter>input['source'] != 'shared'</filter>
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148 </data>
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149 <collection name="trefiles" type="list" label="${tool.name} on ${on_string}: tre">
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150 <filter>input['source'] == 'shared'</filter>
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151 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.tre" format="mothur.tre"/>
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152 </collection>
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153 </outputs>
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154 <tests>
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155 <test><!-- test with phylip and defaults -->
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156 <param name="source" value="phylip"/>
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157 <param name="dist" value="env.dist"/>
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158 <output name="tre" md5="c74a88ed448aad2d07059eda0b4161e9" ftype="mothur.tre"/>
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159 <expand macro="logfile-test"/>
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160 </test>
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161 <test><!-- test with shared and subsampling -->
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162 <param name="source" value="shared"/>
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163 <param name="dist" value="amazon.an.shared"/>
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164 <param name="use" value="yes"/>
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165 <param name="calc" value="jclass"/>
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166 <output_collection name="trefiles" count="108">
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167 <element name="jclass.0.32.all" md5="b8adfa6e41397b3815768f987836d102" ftype="mothur.tre"/>
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168 </output_collection>
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169 <expand macro="logfile-test"/>
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170 </test>
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171 <test><!-- test with shared and label and group select and all calculators -->
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172 <param name="source" value="shared"/>
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173 <param name="dist" value="amazon.an.shared"/>
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174 <param name="label" value="0.05,0.22,0.32"/>
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175 <param name="groups" value="forest,pasture"/>
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176 <param name="calc" value="sharedsobs,sharedchao,sharedace,anderberg,jclass,jest,kulczynski,kulczynskicody,kstest,lennon,ochiai,sorclass,sorest,whittaker,hamming,memchi2,memchord,memeuclidean,mempearson,braycurtis,jabund,morisitahorn,sorabund,thetan,thetayc,canberra,gower,hellinger,manhattan,odum,soergel,spearman,speciesprofile,structchi2,structchord,structeuclidean,structkulczynski,structpearson,sharednseqs,sharedobserved"/>
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177 <output_collection name="trefiles" count="117">
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178 <element name="canberra.0.32" md5="477b061d738d24a7476dd4c90d9666cf" ftype="mothur.tre"/>
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179 </output_collection>
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180 <expand macro="logfile-test"/>
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181 </test>
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182 <test><!-- test with column and name file -->
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183 <param name="source" value="column"/>
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184 <param name="dist" value="amazon.pair.dist"/>
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185 <param name="name" value="amazon1.names"/>
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186 <output name="tre" md5="33cc8cb433f123e49b33b998186b74ed" ftype="mothur.tre"/>
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187 <expand macro="logfile-test"/>
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188 </test>
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189 </tests>
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190 <help>
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191 <![CDATA[
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192
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193 @MOTHUR_OVERVIEW@
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194
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195 **Command Documenation**
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196
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197 The tree.shared_ command will generate a newick-formatted tree file that describes the dissimilarity (1-similarity) among multiple groups. For calc parameter choices see: http://www.mothur.org/wiki/Calculators
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198
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199 .. _tree.shared: http://www.mothur.org/wiki/Tree.shared
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200
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201 ]]>
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202 </help>
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203 <expand macro="citations"/>
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204 </tool>