Mercurial > repos > iuc > mothur_heatmap_sim

annotate heatmap.sim.xml @ 4:2f93c7bba6f8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit be5c8af076296a53959fc3ed2b82d92dc7607eeb
author iuc
date Mon, 23 Apr 2018 09:48:42 -0400
parents 6c7e2e05f606
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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002aec843953 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_heatmap_sim" name="Heatmap.sim" version="@WRAPPER_VERSION@.0">
002aec843953 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Generate a heatmap for pariwise similarity</description>
002aec843953 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros>
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4 <import>macros.xml</import>
002aec843953 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
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6 <expand macro="requirements"/>
002aec843953 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
2
6c7e2e05f606 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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10 @SHELL_OPTIONS@
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11
2
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12 ## create symlinks to input datasets
6c7e2e05f606 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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13 ln -s '$count' count.dat &&
6c7e2e05f606 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 #if $input.source == 'shared':
6c7e2e05f606 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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15 ln -s '$input.otu' input_otu.dat &&
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16 #else
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17 ln -s '$input.dist' input_dist.dat &&
6c7e2e05f606 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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18 #if $input.source == 'column':
6c7e2e05f606 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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19 ln -s '$input.name' input_name.dat &&
6c7e2e05f606 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 #end if
0
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22
2
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23 echo 'heatmap.sim(
6c7e2e05f606 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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24 #if $input.source == "shared":
6c7e2e05f606 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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25 shared=input_otu.dat,
6c7e2e05f606 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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26 #if $input.label:
6c7e2e05f606 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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27 label=${ str($input.label).replace(",","-") },
6c7e2e05f606 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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28 #end if
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29 #if $input.groups:
6c7e2e05f606 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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30 groups=${ str($input.groups).replace(",","-") },
6c7e2e05f606 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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31 #end if
6c7e2e05f606 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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32 #if $input.calc:
6c7e2e05f606 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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33 calc=${ str($input.calc).replace(",","-") },
6c7e2e05f606 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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34 #end if
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35 #elif $input.source == "column":
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36 column=input_dist.dat,
6c7e2e05f606 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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37 name=input_name.dat,
6c7e2e05f606 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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38 #elif $input.source == "phylip":
6c7e2e05f606 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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39 phylip=input_dist.dat,
6c7e2e05f606 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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40 #end if
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41 #if $count:
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42 count=count.dat,
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43 #end if
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44 fontsize=$fontsize
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45 )'
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46 | sed 's/ //g' ## mothur trips over whitespace
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47 | mothur
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48 | tee mothur.out.log
0
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49 ]]></command>
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50 <inputs>
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51 <conditional name="input">
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52 <param name="source" type="select" label="Generate Heatmap for">
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53 <option value="shared">shared - Sample Similarity - OTU Shared</option>
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54 <option value="phylip">phylip - Phylip Distance Matrix</option>
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55 <option value="column">colomn - Pairwise Column Distance Matrix</option>
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56 </param>
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57 <when value="shared">
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58 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
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59 <param name="label" type="select" label="label - OTU Labels" multiple="true">
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60 <expand macro="labeloptions"/>
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61 </param>
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62 <param name="groups" type="select" multiple="true" label="groups - Groups to include">
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63 <options>
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64 <filter type="data_meta" ref="otu" key="groups"/>
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65 </options>
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66 </param>
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67 <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none selected)">
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68 <option value="jclass">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
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69 <option value="jest" selected="true">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</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="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
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73 <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
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74 <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
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75 <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
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76 <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
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77 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
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78 </param>
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79 </when>
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80 <when value="column">
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81 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
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82 <param name="name" type="data" format="mothur.names" label="name - Names"/>
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83 </when>
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84 <when value="phylip">
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85 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
002aec843953 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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86 </when>
002aec843953 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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87 </conditional>
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88 <param name="fontsize" type="integer" value="24" min="0" max="100" label="fontsize - Fontsize (default is 24)"/>
002aec843953 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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89 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count table" help="generated by count.seqs"/>
2
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90 <expand macro="param-savelog"/>
0
002aec843953 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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91 </inputs>
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92 <outputs>
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93 <expand macro="logfile-output"/>
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94 <data name="heatmap" format="svg" from_work_dir="input_dist*.heatmap.sim.svg" label="${tool.name} on ${on_string}: heatmap.sim.svg">
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95 <filter>input['source'] != 'shared'</filter>
002aec843953 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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96 </data>
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97 <collection name="heatmaps" type="list" label="${tool.name} on ${on_string}: Heatmaps">
002aec843953 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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98 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.sim\.svg"/>
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99 <filter>input['source'] == 'shared'</filter>
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100 </collection>
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101 </outputs>
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102 <tests>
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103 <test>
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104 <param name="source" value="phylip"/>
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105 <param name="dist" value="amazon.dist" ftype="mothur.square.dist"/>
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106 <output name="heatmap">
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107 <assert_contents>
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108 <has_text text="svg xmlns:svg="/>
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109 <has_text text="Heatmap for"/>
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110 <has_text text="U68640"/>
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111 </assert_contents>
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112 </output>
2
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113 <param name="savelog" value="true"/>
0
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114 <expand macro="logfile-test"/>
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115 </test>
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116 <test>
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117 <param name="source" value="shared"/>
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118 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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119 <output_collection name="heatmaps" count="72">
2
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120 <element name="0.55.jest.heatmap">
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121 <assert_contents>
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122 <has_text text="svg xmlns:svg="/>
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123 <has_text text="Heatmap at distance 0.55"/>
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124 </assert_contents>
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125 </element>
0
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126 </output_collection>
2
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127 <param name="savelog" value="true"/>
0
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128 <expand macro="logfile-test"/>
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129 </test>
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130 <test>
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131 <param name="source" value="shared"/>
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132 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
002aec843953 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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133 <param name="label" value="0.03,0.26,0.55"/>
002aec843953 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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134 <param name="calc" value="jclass,jest,sorclass,sorest,braycurtis,jabund,morisitahorn,sorabund,thetan,thetayc"/>
002aec843953 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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135 <param name="groups" value="forest,pasture"/>
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136 <output_collection name="heatmaps" count="30">
2
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137 <element name="0.03.braycurtis.heatmap">
6c7e2e05f606 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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138 <assert_contents>
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139 <has_text text="svg xmlns:svg="/>
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140 <has_text text="Heatmap at distance 0.03"/>
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141 </assert_contents>
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142 </element>
0
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143 </output_collection>
2
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144 <param name="savelog" value="true"/>
0
002aec843953 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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145 <expand macro="logfile-test"/>
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146 </test>
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147 </tests>
2
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148 <help><![CDATA[
0
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149
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150 @MOTHUR_OVERVIEW@
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151
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152 **Command Documentation**
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153
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154 The heatmap.sim_ command generates a heat map from data provided in either a shared_ file, a phylip_ distance matrix, or a column_ distance matrix and a name_ file. For calc parameter choices see: https://www.mothur.org/wiki/Calculators
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155
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156 .. _shared: https://www.mothur.org/wiki/Shared_file
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157 .. _phylip: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
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158 .. _column: https://www.mothur.org/wiki/Column-formatted_distance_matrix
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159 .. _name: https://www.mothur.org/wiki/Name_file
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160 .. _heatmap.sim: https://www.mothur.org/wiki/Heatmap.sim
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161
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162 v.1.24.0: Updated to Mothur 1.33, added count parameter
2
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163
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164 ]]></help>
0
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165 <expand macro="citations"/>
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166 </tool>