Mercurial > repos > jjohnson > mothur_toolsuite

annotate mothur/tools/mothur/tree.shared.xml @ 27:49058b1f8d3f

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Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
author Jim Johnson <jj@umn.edu>
date Tue, 04 Dec 2012 11:05:19 -0600
parents 5c77423823cb
children 95d75b35e4d2
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26
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1 <tool id="mothur_tree_shared" name="Tree.shared" version="1.25.0" force_history_refresh="True">
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2 <description>Generate a newick tree for dissimilarity among groups</description>
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3 <command interpreter="python">
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4 mothur_wrapper.py
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5 --cmd='tree.shared'
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6 #if $input.source == 'shared':
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7 --result='^mothur.\S+\.logfile$:'$logfile
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8 #if $input.as_datasets.__str__ == "yes":
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9 --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
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10 --new_datasets='^\S+?([a-z]+\.(unique|[0-9.]*)(\.(all|ave|cons))?\.tre)$:tre'
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11 #end if
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12 --shared=$input.dist
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13 #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
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14 --groups=$input.groups
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15 #end if
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16 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
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17 --label='$input.label'
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18 #end if
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5c77423823cb Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)
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19 #if $input.subsampling.use:
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20 #if len($input.subsampling.subsample.__str__) > 0 and int($input.subsampling.subsample.__str__) > 0:
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21 --subsample=$input.subsampling.subsample
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22 #else
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23 --subsample=T
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24 #end if
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25 #if len($input.subsampling.iters.__str__) > 0 and int($input.subsampling.iters.__str__) > 0:
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26 --iters=$input.subsampling.iters
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27 #end if
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28 #end if
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29 #else:
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30 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.tre$:'$tre
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31 --outputdir='$logfile.extra_files_path'
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32 #if $input.source == 'column':
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33 --column=$input.dist
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34 --name=$input.name
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35 #elif $input.source == 'phylip':
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36 --phylip=$input.dist
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37 #if $input.name.__str__ != "None" and len($input.name.__str__) > 0:
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38 --name=$input.name
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39 #end if
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40 #end if
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41 #end if
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42 #if $calc.__str__ != "None" and len($calc.__str__) > 0:
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43 --calc=$calc
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44 #end if
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45 --processors=8
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46 </command>
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47 <inputs>
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48 <!-- column,name phylip or shared -->
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49 <conditional name="input">
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50 <param name="source" type="select" label="Select input format">
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51 <option value="shared">OTU Shared</option>
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52 <option value="column">Pairwise Column Distance Matrix</option>
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53 <option value="phylip">Phylip Distance Matrix</option>
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54 </param>
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55 <when value="column">
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56 <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/>
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57 <param name="name" type="data" format="names" label="name - Sequences Name reference"/>
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58 </when>
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59 <when value="phylip">
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60 <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/>
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61 <param name="name" type="data" format="names" optional="true" label="name - Names"/>
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62 </when>
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63 <when value="shared">
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64 <param name="dist" type="data" format="shared" label="shared - OTU Shared"/>
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65 <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Create a new history dataset for each label and calculator"/>
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66 <param name="label" type="select" label="label - OTU Labels" multiple="true">
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67 <options>
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68 <filter type="data_meta" ref="dist" key="labels" />
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69 </options>
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70 </param>
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71 <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
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72 <options>
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73 <filter type="data_meta" ref="dist" key="groups" />
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74 </options>
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75 </param>
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76 <conditional name="subsampling">
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77 <param name="use" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="subsample"/>
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78 <when value="yes">
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79 <param name="subsample" type="integer" value="" optional="true" label="subsample (defaults to the size of the smallest group)"
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80 help="Should not exceed the number of sequences in any group"/>
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81 <param name="iters" type="integer" value="" optional="true" label="iters - Number of iterations to try (default 1000)">
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82 <validator type="in_range" message="Number of iterations must be positive" min="1"/>
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83 </param>
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84 </when>
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85 <when value="no"/>
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86 </conditional> <!-- subsampling -->
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87 </when>
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88 </conditional>
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89 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
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90 <option value="sharedsobs">sharedsobs - Shared community richness the observed richness shared between two or more samples</option>
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91 <option value="sharedchao">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option>
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92 <option value="sharedace">sharedace - Shared community richness the two sample shared ACE richness estimator</option>
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93 <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option>
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94 <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
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95 <option value="jest">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option>
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96 <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option>
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97 <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option>
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98 <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option>
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99 <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option>
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100 <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option>
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101 <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
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102 <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option>
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103 <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>
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104 <option value="hamming">hamming - Community Membership Similarity -</option>
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105 <option value="memchi2">memchi2 - Community Membership Similarity -</option>
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106 <option value="memchord">memchord - Community Membership Similarity -</option>
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107 <option value="memeuclidean">memeuclidean - Community Membership Similarity -</option>
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108 <option value="mempearson">mempearson - Community Membership Similarity -</option>
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109 <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
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110 <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
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111 <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
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112 <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
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113 <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
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ed906f8149bb Mothur - html escape amperand in calculator option label
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114 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
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115 <option value="canberra">canberra - Community Structure Similarity -</option>
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116 <option value="gower">gower - Community Structure Similarity -</option>
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117 <option value="hellinger">hellinger - Community Structure Similarity -</option>
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118 <option value="manhattan">manhattan - Community Structure Similarity -</option>
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119 <option value="odum">odum - Community Structure Similarity -</option>
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120 <option value="soergel">soergel - Community Structure Similarity -</option>
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121 <option value="spearman">spearman - Community Structure Similarity -</option>
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122 <option value="speciesprofile">speciesprofile - Community Structure Similarity -</option>
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123 <option value="structchi2">structchi2 - Community Structure Similarity -</option>
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124 <option value="structchord">structchord - Community Structure Similarity -</option>
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125 <option value="structeuclidean">structeuclidean - Community Structure Similarity -</option>
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126 <option value="structkulczynski">structkulczynski - Community Structure Similarity -</option>
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127 <option value="structpearson">structpearson - Community Structure Similarity -</option>
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128 <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option>
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129 <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option>
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130 </param>
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131 </inputs>
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132 <outputs>
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133 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
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134 <data format="tre" name="tre" label="${tool.name} on ${on_string}: tre">
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135 <filter>input['source'] != 'shared'</filter>
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136 </data>
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137 </outputs>
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138 <requirements>
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139 <requirement type="package" version="1.27">mothur</requirement>
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140 </requirements>
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141 <tests>
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142 </tests>
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143 <help>
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144 **Mothur Overview**
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145
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146 Mothur_, initiated by Dr. Patrick Schloss and his software development team
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147 in the Department of Microbiology and Immunology at The University of Michigan,
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148 provides bioinformatics for the microbial ecology community.
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149
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150 .. _Mothur: http://www.mothur.org/wiki/Main_Page
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151
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152 **Command Documenation**
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153
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154 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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155
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156 .. _tree.shared: http://www.mothur.org/wiki/Tree.shared
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157
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158
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159 </help>
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160 </tool>