Mercurial > repos > iuc > mothur_dist_shared

annotate dist.shared.xml @ 10:418100660ba3 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
author iuc
date Mon, 17 Jun 2024 12:23:10 +0000
parents b7da1494afa1
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7773b7afb53d 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_dist_shared" name="Dist.shared" version="@WRAPPER_VERSION@.0">
7773b7afb53d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Generate a phylip-formatted dissimilarity distance matrix among multiple groups</description>
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3 <macros>
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4 <import>macros.xml</import>
7773b7afb53d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
10
418100660ba3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
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6 <expand macro="biotools"/>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <expand macro="version_command"/>
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10 <command><![CDATA[
2
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11 @SHELL_OPTIONS@
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12
2
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13 ## create symlinks to input datasets
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14 ln -s '$otu' otu.dat &&
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15
2
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16 echo 'dist.shared(
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17 shared=otu.dat,
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18 #if $label:
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19 label=${ str($label).replace(",","-") },
b7da1494afa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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20 #end if
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21 #if $groups:
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22 groups=${ str($groups).replace(",","-") },
b7da1494afa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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23 #end if
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24 #if $calc:
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25 calc=${ str($calc).replace(",","-") },
b7da1494afa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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26 #end if
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27 #if $subsampling.use == "yes":
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28 #if $subsampling.subsample:
b7da1494afa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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29 subsample=$subsampling.subsample,
b7da1494afa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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30 #else
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31 subsample=T,
b7da1494afa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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32 #end if
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33 iters=$subsampling.iters,
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34 #end if
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35 output=$output,
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36 processors='\${GALAXY_SLOTS:-8}'
b7da1494afa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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37 )'
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38 | sed 's/ //g' ## mothur trips over whitespace
b7da1494afa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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39 | mothur
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40 | tee mothur.out.log
0
7773b7afb53d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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41 ]]></command>
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42 <inputs>
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43 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
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44 <param name="label" type="select" label="label - OTU Labels to calculate" multiple="true">
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45 <expand macro="labeloptions"/>
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46 </param>
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47 <param name="groups" type="select" label="groups - Groups to analyze" multiple="true">
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48 <options>
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49 <filter type="data_meta" ref="otu" key="groups"/>
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50 </options>
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51 </param>
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52 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
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53 <expand macro="calc-common"/>
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54 <!-- set default option(s) -->
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55 <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
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56 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
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57 </param>
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58 <conditional name="subsampling">
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59 <param name="use" type="select" label="subsample">
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60 <option value="no" selected="true">no</option>
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61 <option value="yes">yes</option>
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62 </param>
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63 <when value="yes">
2
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64 <param name="subsample" type="integer" value="" min="0" optional="true" label="subsample (defaults to the size of the smallest group)"
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65 help="Should not exceed the number of sequences in any group"/>
0
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66 <param name="iters" type="integer" value="1000" min="1" optional="true" label="iters - Number of iterations to try (default 1000)"/>
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67 </when>
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68 <when value="no"/>
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69 </conditional>
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70 <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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71 <option value="lt" selected="true">Phylip formatted Lower Triangle Matrix</option>
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72 <option value="square">Phylip formatted Square Matrix</option>
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73 </param>
2
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74 <expand macro="param-savelog"/>
0
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75 </inputs>
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76 <outputs>
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77 <expand macro="logfile-output"/>
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78 <collection name="distfiles" type="list" label="${tool.name} on ${on_string}: dist files">
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79 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.dist" format="mothur.dist"/>
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80 </collection>
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81 </outputs>
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82 <tests>
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83 <test><!-- test with defaults -->
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84 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
7773b7afb53d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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85 <output_collection name="distfiles" count="72">
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86 <element name="thetayc.0.33.lt" md5="c707e43f14c2022f4027e6a2495cbae8" ftype="mothur.dist"/>
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87 </output_collection>
2
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88 <param name="savelog" value="true"/>
0
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89 <expand macro="logfile-test"/>
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90 </test>
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91 <test><!-- test with label,group select and all calculators -->
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92 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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93 <param name="label" value="0.05,0.22"/>
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94 <param name="groups" value="forest,pasture"/>
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95 <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,structeuclidean,structpearson,sharednseqs,sharedobserved"/>
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96 <output_collection name="distfiles" count="74">
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97 <element name="gower.0.22.lt" md5="209dbf7e9f1e13753524905f64c8e3b7" ftype="mothur.dist"/>
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98 </output_collection>
2
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99 <param name="savelog" value="true"/>
0
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100 <expand macro="logfile-test"/>
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101 </test>
2
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102 <test><!-- test with subsampling without specifying size -->
0
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103 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
2
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104 <param name="label" value="0.03,0.33"/>
0
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105 <param name="use" value="yes"/>
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106 <param name="calc" value="canberra"/>
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107 <param name="output" value="square"/>
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108 <output_collection name="distfiles" count="6">
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109 <element name="canberra.0.33.square.std" ftype="mothur.dist">
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110 <assert_contents>
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111 <has_text text="forest"/>
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112 <has_text text="pasture"/>
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113 </assert_contents>
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114 </element>
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115 </output_collection>
2
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116 <param name="savelog" value="true"/>
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117 <expand macro="logfile-test"/>
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118 </test>
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119 <test><!-- test with subsampling with specifying size-->
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120 <param name="otu" value="amazon.mothur.shared" ftype="mothur.shared"/>
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121 <param name="use" value="yes"/>
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122 <param name="subsample" value="2"/>
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123 <param name="iters" value="42"/>
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124 <param name="label" value="0.10"/>
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125 <param name="calc" value="canberra"/>
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126 <param name="output" value="square"/>
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127 <output_collection name="distfiles" count="3">
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128 <element name="canberra.0.10.square.std" ftype="mothur.dist">
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129 <assert_contents>
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130 <has_text text="forest"/>
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131 <has_text text="pasture"/>
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132 </assert_contents>
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133 </element>
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134 </output_collection>
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135 <param name="savelog" value="true"/>
0
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136 <expand macro="logfile-test"/>
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137 </test>
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138 </tests>
2
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139 <help><![CDATA[
0
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140
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141 @MOTHUR_OVERVIEW@
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142
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143 **Command Documentation**
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144
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145 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: https://www.mothur.org/wiki/Calculators
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146
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147 .. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
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148 .. _shared: https://www.mothur.org/wiki/Shared_file
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149 .. _dist.shared: https://www.mothur.org/wiki/Dist.shared
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150
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151 v1.26.0: Updated to Mothur 1.33. Omitted calculators since they do not appear to be available.
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152
2
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153 ]]></help>
0
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154 <expand macro="citations"/>
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155 </tool>