Mercurial > repos > iuc > qiime_alpha_rarefaction

annotate alpha_rarefaction.xml @ 7:9023dcdccf72 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c"
author iuc
date Thu, 05 Dec 2019 07:46:03 -0500
parents 0a097fc6e5a6
children
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9023dcdccf72 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c"
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1 <tool id="qiime_alpha_rarefaction" name="Perform alpha rarefaction" version="@WRAPPER_VERSION@.0" profile="@PROFILE@">
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2 <description>(alpha_rarefaction)</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>alpha_rarefaction.py --version</version_command>
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8 <command detect_errors="aggressive"><![CDATA[
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9 @MPLBACKEND@
5
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10 alpha_rarefaction.py
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11 --otu_table_fp '$otu_table_fp'
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12 --mapping_fp '$mapping_fp'
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13 -o alpha_rarefaction
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14 #if $parameter_fp
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15 --parameter_fp '$parameter_fp'
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16 #end if
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17 --num_steps '$num_steps'
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18 $parallel
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19 -O "\${GALAXY_SLOTS:-4}"
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20 #if $tree_fp
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21 --tree_fp '$tree_fp'
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22 #end if
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23 --min_rare_depth '$min_rare_depth'
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24 #if $max_rare_depth
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25 --max_rare_depth '$max_rare_depth'
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26 #end if
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27 $retain_intermediate_files
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28
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29 && mkdir -p $alpha_rarefaction_plots.files_path
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30 && cp alpha_rarefaction/alpha_rarefaction_plots/rarefaction_plots.html $alpha_rarefaction_plots
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31 && cp -r alpha_rarefaction/alpha_rarefaction_plots/average_plots $alpha_rarefaction_plots.files_path
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32 ]]></command>
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33 <inputs>
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34 <param argument="--otu_table_fp" type="data" format="tabular,txt,tsv,biom" label="OTU table"/>
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35 <param argument="--mapping_fp" type="data" format="tabular,txt,tsv" label="Mapping file"/>
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36 <param argument="--parameter_fp" type="data" format="txt" optional="true" label="Parameter file" help="It specifies changes to the default behavior"/>
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37 <param argument="--num_steps" type="integer" value="10" label="Number of steps (or rarefied OTU table sizes) to make between min and max counts"/>
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38 <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="true" label="Run in parallel where available?"/>
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39 <param argument="--tree_fp" type="data" format="tabular,txt,tsv" optional="true" label="Tree file (optional)" help="Required for phylogenetic measures"/>
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40 <param argument="--min_rare_depth" type="integer" value="10" label="Lower limit of rarefaction depths"/>
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41 <param argument="--max_rare_depth" type="integer" label="Upper limit of rarefaction depths" help="By default, median sequence/sample count is used" optional="True"/>
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42 <param argument="--retain_intermediate_files" type="boolean" truevalue="--retain_intermediate_files" falsevalue="" checked="true" label="Retain intermediate files?"/>
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43 </inputs>
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44 <outputs>
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45 <data name="alpha_rarefaction_plots" format="html" label="${tool.name} on ${on_string}: Alpha rarefaction plots"/>
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46 <collection name="alpha_diversity" type="list" label="${tool.name} on ${on_string}: Alpha diversity information">
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47 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" directory="alpha_rarefaction/alpha_div_collated/"/>
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48 </collection>
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49 <collection name="rarefaction" type="list" label="${tool.name} on ${on_string}: Rarefied OTU tables">
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50 <discover_datasets pattern="rarefaction_(?P&lt;designation&gt;.+)\.biom" directory="alpha_rarefaction/rarefaction/"/>
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51 <filter>retain_intermediate_files!=''</filter>
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52 </collection>
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53 <collection name="alpha_div" type="list" label="${tool.name} on ${on_string}: Alpha diversity results">
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54 <discover_datasets pattern="alpha_rarefaction_(?P&lt;designation&gt;.+)\.txt" directory="alpha_rarefaction/alpha_div/"/>
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55 <filter>retain_intermediate_files!=''</filter>
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56 </collection>
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57 </outputs>
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58 <tests>
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59 <test>
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60 <param name="otu_table_fp" value="alpha_rarefaction/otu_table.biom"/>
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61 <param name="mapping_fp" value="alpha_rarefaction/mapping_file.txt"/>
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62 <param name="num_steps" value="2"/>
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63 <param name="parallel" value=""/>
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64 <param name="tree_fp" value="alpha_rarefaction/rep_set.tre"/>
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65 <param name="min_rare_depth" value="10"/>
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66 <param name="max_rare_depth" value="50"/>
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67 <param name="retain_intermediate_files" value="--retain_intermediate_files"/>
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68 <output name="alpha_rarefaction_plots">
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69 <assert_contents>
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70 <has_text text="Control_mouse_I.D._354" />
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71 </assert_contents>
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72 </output>
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73 <output_collection name="alpha_diversity" type="list" count="3">
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74 <element name="chao1">
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75 <assert_contents>
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76 <has_text text="alpha_rarefaction_10_0" />
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77 <has_text text="alpha_rarefaction_30_5" />
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78 <has_text text="alpha_rarefaction_50_9" />
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79 </assert_contents>
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80 </element>
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81 <element name="observed_otus">
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82 <assert_contents>
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83 <has_text text="alpha_rarefaction_10_0" />
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84 <has_text text="alpha_rarefaction_30_5" />
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85 <has_text text="alpha_rarefaction_50_9" />
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86 </assert_contents>
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87 </element>
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88 <element name="PD_whole_tree">
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89 <assert_contents>
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90 <has_text text="alpha_rarefaction_10_0" />
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91 <has_text text="alpha_rarefaction_30_5" />
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92 <has_text text="alpha_rarefaction_50_9" />
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93 </assert_contents>
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94 </element>
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95 </output_collection>
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96 <output_collection name="rarefaction" type="list" count="30">
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97 <element name="10_0">
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98 <assert_contents>
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99 <has_text text="PC.636" />
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100 <has_text text="PC.354" />
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101 <has_text text="PC.634" />
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102 </assert_contents>
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103 </element>
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104 <element name="30_6">
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105 <assert_contents>
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106 <has_text text="PC.636" />
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107 <has_text text="PC.354" />
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108 <has_text text="PC.634" />
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109 </assert_contents>
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110 </element>
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111 <element name="50_9">
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112 <assert_contents>
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113 <has_text text="PC.636" />
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114 <has_text text="PC.354" />
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115 <has_text text="PC.634" />
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116 </assert_contents>
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117 </element>
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118 </output_collection>
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119 <output_collection name="alpha_div" type="list" count="30">
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120 <element name="10_0">
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121 <assert_contents>
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122 <has_text text="PC.636" />
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123 <has_text text="PC.354" />
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124 <has_text text="PC.634" />
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125 </assert_contents>
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126 </element>
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127 <element name="30_6">
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128 <assert_contents>
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129 <has_text text="PC.636" />
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130 <has_text text="PC.354" />
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131 <has_text text="PC.634" />
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132 </assert_contents>
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133 </element>
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134 <element name="50_9">
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135 <assert_contents>
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136 <has_text text="PC.636" />
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137 <has_text text="PC.354" />
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138 <has_text text="PC.634" />
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139 </assert_contents>
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140 </element>
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141 </output_collection>
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142 </test>
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143 </tests>
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144 <help><![CDATA[
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145 **What it does**
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146
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147 This script performs alpha rarefaction in several steps:
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148
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149 - Generation of rarefied OTU tables
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150 - Computation of alpha diversity metrics for each rarefied OTU table
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151 - Concatenation of alpha diversity results
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152 - Generation of alpha rarefaction plots
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153
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154 More information about this tool is available on
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155 `QIIME documentation <http://qiime.org/scripts/alpha_rarefaction.html>`_.
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156 ]]></help>
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157 <citations>
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158 <expand macro="citations"/>
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159 </citations>
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160 </tool>