Mercurial > repos > iuc > qiime_core_diversity

annotate core_diversity_analyses.xml @ 5:486570c88d1b draft

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author iuc
date Sat, 05 Aug 2017 07:14:36 -0400
parents 61e86fd975a4
children 57deb17cadbf
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1 <tool id="qiime_core_diversity" name="Run a core set of QIIME diversity analyses" version="@WRAPPER_VERSION@.0">
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2 <description>(core_diversity_analyses)</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 <version_command>core_diversity_analyses.py --version</version_command>
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8 <command detect_errors="aggressive"><![CDATA[
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9 ## set matplotlib backend
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10 echo "backend:agg" > matplotlibrc &&
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11
5
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12 core_diversity_analyses.py
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13 --input_biom_fp '$input_biom_fp'
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14 -o core_diversity_analyses
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15 --mapping_fp '$mapping_fp'
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16 --sampling_depth '$sampling_depth'
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17 #if $parameter_fp
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18 --parameter_fp '$parameter_fp'
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19 #end if
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20 $parallel
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21 -O "\${GALAXY_SLOTS:-4}"
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22 $phylogenetic.nonphylogenetic_diversity
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23 #if str( $phylogenetic.nonphylogenetic_diversity ) == ""
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24 --tree_fp '$phylogenetic.tree_fp'
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25 #end if
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26 $suppress_taxa_summary
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27 $suppress_beta_diversity
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28 $suppress_alpha_diversity
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29 $suppress_group_significance
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30 #if str( $categories ):
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31 --categories '$categories'
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32 #end if
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33
5
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34 && mkdir -p '$html_report.files_path'
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35 && cp -r core_diversity_analyses/* '$html_report.files_path'
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36 && mv '$html_report.files_path/index.html' '$html_report'
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37 ]]></command>
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38 <inputs>
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39 <param argument="--input_biom_fp" type="data" format="tabular,txt,biom,h5" label="OTU table"/>
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40 <param argument="--mapping_fp" type="data" format="tabular,txt,tsv" label="Mapping file" />
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41 <param argument="--sampling_depth" type="integer" value="" label="Sequencing depth to use for even sub-sampling and maximum rarefaction depth" help="To decide this value, review the output of the ‘biom summarize-table’"/>
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42 <param argument="--parameter_fp" type="data" format="txt" label="Parameter file" help="It specifies changes to the default behavior" optional="true"/>
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43 <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="true" label="Run in parallel where available?"/>
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44 <conditional name="phylogenetic">
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45 <param argument="--nonphylogenetic_diversity" type="select" label="Apply non-phylogenetic alpha (chao1 and observed_otus) and beta (bray_curtis) diversity calculations?" help="This is useful if, for example, when working with non-amplicon BIOM tables, or if a reliable tree is not available">
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46 <option value="--nonphylogenetic_diversity">Yes</option>
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47 <option value="" selected="true">No</option>
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48 </param>
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49 <when value="">
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50 <param argument="--tree_fp" type="data" format="txt" label="Tree file"/>
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51 </when>
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52 <when value="--nonphylogenetic_diversity"/>
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53 </conditional>
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54 <param argument="--suppress_taxa_summary" type="boolean" truevalue="--suppress_taxa_summary" falsevalue="" checked="false" label="Suppress generation of taxa summary plots?"/>
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55 <param argument="--suppress_beta_diversity" type="boolean" truevalue="--suppress_beta_diversity" falsevalue="" checked="false" label="Suppress beta diversity analyses?"/>
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56 <param argument="--suppress_alpha_diversity" type="boolean" truevalue="--suppress_alpha_diversity" falsevalue="" checked="false" label="Suppress alpha diversity analyses?"/>
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57 <param argument="--suppress_group_significance" type="boolean" truevalue="--suppress_group_significance" falsevalue="" checked="false" label="Suppress OTU/category significance analysis?"/>
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58 <param argument="--categories" type="text" value="" optional="true" label="Metadata category or categories to compare for categorical analyses (optional)" help="The column headers in the mapping file should be passed as a comma-separated list. By default, no categorical analyses are performed"/>
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59 </inputs>
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60 <outputs>
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61 <data name="html_report" format="html" label="${tool.name} on ${on_string}: Core diversity report"/>
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62 </outputs>
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63 <tests>
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64 <test> <!-- test taxa summary and group significance -->
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65 <param name="input_biom_fp" value="core_diversity_analyses/otu_table.biom"/>
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66 <param name="mapping_fp" value="core_diversity_analyses/map.txt"/>
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67 <param name="sampling_depth" value="22"/>
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68 <param name="parallel" value="--parallel"/>
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69 <param name="nonphylogenetic_diversity" value=""/>
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70 <param name="tree_fp" value="core_diversity_analyses/rep_set.tre"/>
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71 <param name="suppress_taxa_summary" value=""/>
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72 <param name="suppress_beta_diversity" value="--suppress_beta_diversity"/>
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73 <param name="suppress_alpha_diversity" value="--suppress_alpha_diversity"/>
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74 <param name="suppress_group_significance" value=""/>
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75 <output name="html_report">
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76 <assert_contents>
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77 <has_text text="Filtered BIOM table (minimum sequence count: 22)"/>
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78 <has_text text="rarefied BIOM table (sampling depth: 22)"/>
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79 <has_text text="Taxa summary bar plots"/>
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80 </assert_contents>
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81 </output>
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82 </test>
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83 <test><!-- test beta diversity -->
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84 <param name="input_biom_fp" value="core_diversity_analyses/otu_table.biom"/>
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85 <param name="mapping_fp" value="core_diversity_analyses/map.txt"/>
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86 <param name="sampling_depth" value="22"/>
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87 <param name="parallel" value="--parallel"/>
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88 <param name="nonphylogenetic_diversity" value="--nonphylogenetic_diversity"/>
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89 <param name="suppress_taxa_summary" value="--suppress_taxa_summary"/>
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90 <param name="suppress_beta_diversity" value=""/>
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91 <param name="suppress_alpha_diversity" value="--suppress_alpha_diversity"/>
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92 <param name="suppress_group_significance" value="--suppress_group_significance"/>
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93 <output name="html_report">
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94 <assert_contents>
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95 <has_text text="Filtered BIOM table (minimum sequence count: 22)"/>
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96 <has_text text="rarefied BIOM table (sampling depth: 22)"/>
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97 <has_text text="Beta diversity results"/>
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98 </assert_contents>
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99 </output>
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100 </test>
3
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101 <test><!-- test alpha diversity -->
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102 <param name="input_biom_fp" value="core_diversity_analyses/otu_table.biom"/>
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103 <param name="mapping_fp" value="core_diversity_analyses/map.txt"/>
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104 <param name="parameter_fp" value="core_diversity_analyses/alpha_diversity_params.txt"/>
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105 <param name="sampling_depth" value="22"/>
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106 <param name="parallel" value="--parallel"/>
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107 <param name="nonphylogenetic_diversity" value="--nonphylogenetic_diversity"/>
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108 <param name="suppress_taxa_summary" value="--suppress_taxa_summary"/>
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109 <param name="suppress_beta_diversity" value="--suppress_beta_diversity"/>
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110 <param name="suppress_alpha_diversity" value=""/>
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111 <param name="suppress_group_significance" value="--suppress_group_significance"/>
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112 <output name="html_report">
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113 <assert_contents>
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114 <has_text text="Filtered BIOM table (minimum sequence count: 22)"/>
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115 <has_text text="rarefied BIOM table (sampling depth: 22)"/>
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116 <has_text text="Alpha rarefaction plots"/>
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117 </assert_contents>
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118 </output>
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119 </test>
0
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120 <test><!-- test suppressing all -->
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121 <param name="input_biom_fp" value="core_diversity_analyses/otu_table.biom"/>
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122 <param name="mapping_fp" value="core_diversity_analyses/map.txt"/>
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123 <param name="sampling_depth" value="22"/>
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124 <param name="parallel" value="--parallel"/>
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125 <param name="nonphylogenetic_diversity" value="--nonphylogenetic_diversity"/>
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126 <param name="suppress_taxa_summary" value="--suppress_taxa_summary"/>
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127 <param name="suppress_beta_diversity" value="--suppress_beta_diversity"/>
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128 <param name="suppress_alpha_diversity" value="--suppress_alpha_diversity"/>
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129 <param name="suppress_group_significance" value="--suppress_group_significance"/>
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130 <output name="html_report">
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131 <assert_contents>
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132 <has_text text="Filtered BIOM table (minimum sequence count: 22)"/>
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133 <has_text text="rarefied BIOM table (sampling depth: 22)"/>
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134 </assert_contents>
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135 </output>
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136 </test>
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137 </tests>
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138 <help><![CDATA[
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139 **What it does**
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140
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141 This tool calculates alpha diversity, or within-sample diversity, using an
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142 OTU table.
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143
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144 The resulting file(s) is a tab-delimited text file, where the columns correspond
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145 to alpha diversity metrics and the rows correspond to samples and their calculated
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146 diversity measurements. When a folder is given as input (-i), the script processes
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147 every otu table file in the given folder, and creates a corresponding file in the
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148 output directory.
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149
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150 More information about this tool is available on
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151 `QIIME documentation <http://qiime.org/scripts/core_diversity_analyses.html>`_.
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152 ]]></help>
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153 <citations>
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154 <expand macro="citations"/>
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155 </citations>
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156 </tool>