Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/dist.shared.xml @ 36:040410b8167e default tip
Fixed reference to legacy blast repository in tool_dependencies.xml. Updated README with author information.
author | galaxyuser <galaxy_user@agr.g.ca> |
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date | Mon, 10 Nov 2014 15:40:02 -0500 |
parents | 95d75b35e4d2 |
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Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
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1 <tool id="mothur_dist_shared" name="Dist.shared" version="1.26.0" force_history_refresh="True"> |
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2 <description>Generate a phylip-formatted dissimilarity distance matrix among multiple groups</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='dist.shared' |
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6 --result='^mothur.\S+\.logfile$:'$logfile |
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7 --outputdir='$logfile.extra_files_path' |
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8 #if $as_datasets.__str__ == "yes": |
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9 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' |
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10 #if len($output.__str__) > 0: |
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11 #if $output.__str__ == 'square': |
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12 --new_datasets='^\S+?\.([a-z]+\.(unique|[0-9.]*)\.(square|lt)(\.(ave|std))?)\.dist$:square.dist' |
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13 #elif $output.__str__ == 'lt': |
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14 --new_datasets='^\S+?\.([a-z]+\.(unique|[0-9.]*)\.(square|lt)(\.(ave|std))?)\.dist$:lower.dist' |
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15 #end if |
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16 #else: |
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17 --new_datasets='^\S+?\.([a-z]+\.(unique|[0-9.]*)\.(square|lt)(\.(ave|std))?)\.dist$:lower.dist' |
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18 #end if |
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19 #end if |
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20 --shared=$otu |
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21 #if $label.__str__ != "None" and len($label.__str__) > 0: |
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22 --label='$label' |
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23 #end if |
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24 #if $groups.__str__ != "None" and len($groups.__str__) > 0: |
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25 --groups=$groups |
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26 #end if |
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27 #if $calc.__str__ != "None" and len($calc.__str__) > 0: |
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28 --calc=$calc |
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29 #end if |
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30 #if $subsampling.use: |
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31 #if len($subsampling.subsample.__str__) > 0 and int($subsampling.subsample.__str__) > 0: |
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32 --subsample=$subsampling.subsample |
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33 #else |
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34 --subsample=T |
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35 #end if |
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36 #if len($subsampling.iters.__str__) > 0 and int($subsampling.iters.__str__) > 0: |
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37 --iters=$subsampling.iters |
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38 #end if |
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39 #end if |
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40 #if $output.__str__ != "None" and len($output.__str__) > 0: |
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41 --output=$output |
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42 #end if |
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43 --processors=8 |
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44 </command> |
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45 <inputs> |
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46 <!-- list,group or shared --> |
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47 <param name="otu" type="data" format="shared" label="shared - OTU Shared"/> |
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48 <param name="label" type="select" label="label - OTU Labels to calculate" multiple="true"> |
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49 <options> |
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50 <filter type="data_meta" ref="otu" key="labels" /> |
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51 </options> |
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52 </param> |
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53 <param name="groups" type="select" label="groups - Groups to analyze" multiple="true"> |
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54 <options> |
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55 <filter type="data_meta" ref="otu" key="groups" /> |
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56 </options> |
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57 </param> |
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58 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> |
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59 <option value="sharedsobs">sharedsobs - Shared community richness the observed richness shared between two or more samples</option> |
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60 <option value="sharedchao">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option> |
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61 <option value="sharedace">sharedace - Shared community richness the two sample shared ACE richness estimator</option> |
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62 <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option> |
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63 <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option> |
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64 <option value="jest">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option> |
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65 <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option> |
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66 <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option> |
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67 <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option> |
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68 <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option> |
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69 <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option> |
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70 <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option> |
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71 <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option> |
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72 <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option> |
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73 <option value="hamming">hamming - Community Membership Similarity -</option> |
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74 <option value="memchi2">memchi2 - Community Membership Similarity -</option> |
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75 <option value="memchord">memchord - Community Membership Similarity -</option> |
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76 <option value="memeuclidean">memeuclidean - Community Membership Similarity -</option> |
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77 <option value="mempearson">mempearson - Community Membership Similarity -</option> |
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78 <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option> |
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79 <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option> |
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80 <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option> |
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81 <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option> |
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82 <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option> |
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83 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue & Clayton theta similarity coefficient</option> |
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84 <option value="canberra">canberra - Community Structure Similarity -</option> |
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85 <option value="gower">gower - Community Structure Similarity -</option> |
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86 <option value="hellinger">hellinger - Community Structure Similarity -</option> |
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87 <option value="manhattan">manhattan - Community Structure Similarity -</option> |
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88 <option value="odum">odum - Community Structure Similarity -</option> |
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89 <option value="soergel">soergel - Community Structure Similarity -</option> |
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90 <option value="spearman">spearman - Community Structure Similarity -</option> |
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91 <option value="speciesprofile">speciesprofile - Community Structure Similarity -</option> |
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92 <option value="structchi2">structchi2 - Community Structure Similarity -</option> |
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93 <option value="structchord">structchord - Community Structure Similarity -</option> |
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94 <option value="structeuclidean">structeuclidean - Community Structure Similarity -</option> |
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95 <option value="structkulczynski">structkulczynski - Community Structure Similarity -</option> |
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96 <option value="structpearson">structpearson - Community Structure Similarity -</option> |
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97 <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option> |
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98 <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option> |
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99 </param> |
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100 <conditional name="subsampling"> |
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101 <param name="use" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="subsample"/> |
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102 <when value="yes"> |
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103 <param name="subsample" type="integer" value="" optional="true" label="subsample (defaults to the size of the smallest group)" |
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104 help="Should not exceed the number of sequences in any group"/> |
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105 <param name="iters" type="integer" value="" optional="true" label="iters - Number of iterations to try (default 1000)"> |
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106 <validator type="in_range" message="Number of iterations must be positive" min="1"/> |
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107 </param> |
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108 </when> |
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109 <when value="no"/> |
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110 </conditional> <!-- subsampling --> |
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111 <param name="output" type="select" label="output - Distance Matrix Output Format" help="A Distance Matrix will be generated for each calculator label pair"> |
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112 <option value="lt">Phylip formatted Lower Triangle Matrix</option> |
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113 <option value="square">Phylip formatted Square Matrix</option> |
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114 </param> |
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115 <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Create a new history dataset for each distance matrix"/> |
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116 </inputs> |
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117 <outputs> |
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118 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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119 </outputs> |
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120 <requirements> |
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121 <requirement type="package" version="1.33">mothur</requirement> |
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122 </requirements> |
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123 <tests> |
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124 </tests> |
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125 <help> |
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126 **Mothur Overview** |
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127 |
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128 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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129 in the Department of Microbiology and Immunology at The University of Michigan, |
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130 provides bioinformatics for the microbial ecology community. |
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131 |
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132 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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133 |
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134 **Command Documenation** |
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135 |
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136 The dist.shared_ command will generate a phylip-formatted_distance_matrix_ that describes the dissimilarity (1-similarity) among multiple groups from a shared_ file. For calc parameter choices see: http://www.mothur.org/wiki/Calculators |
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137 |
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138 .. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix |
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139 .. _shared: http://www.mothur.org/wiki/Shared_file |
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140 .. _dist.shared: http://www.mothur.org/wiki/Dist.shared |
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141 |
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142 v1.26.0: Updated to Mothur 1.33. Omitted calculators since they do not appear to be available. |
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143 |
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144 |
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145 </help> |
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146 </tool> |