Mercurial > repos > iuc > qiime_alpha_rarefaction

annotate alpha_rarefaction.xml @ 0:d493a0d5d5f5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
author iuc
date Thu, 18 May 2017 09:36:01 -0400
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children 0a097fc6e5a6
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0
d493a0d5d5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
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1 <tool id="qiime_alpha_rarefaction" name="Perform alpha rarefaction" version="@WRAPPER_VERSION@.0">
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2 <description>A workflow script for performing 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 ## set matplotlib backend
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10 echo "backend:agg" > matplotlibrc &&
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11
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12 alpha_rarefaction.py
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13 --otu_table_fp '$otu_table_fp'
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14 --mapping_fp '$mapping_fp'
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15 -o alpha_rarefaction
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16 #if $parameter_fp
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17 --parameter_fp '$parameter_fp'
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18 #end if
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19 --num_steps '$num_steps'
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20 $parallel
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21 -O "\${GALAXY_SLOTS:-4}"
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22 #if $tree_fp
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23 --tree_fp '$tree_fp'
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24 #end if
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25 --min_rare_depth '$min_rare_depth'
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26 #if $max_rare_depth
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27 --max_rare_depth '$max_rare_depth'
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28 #end if
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29 $retain_intermediate_files
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30
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31 && mkdir -p $alpha_rarefaction_plots.files_path
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32 && cp alpha_rarefaction/alpha_rarefaction_plots/rarefaction_plots.html $alpha_rarefaction_plots
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33 && cp -r alpha_rarefaction/alpha_rarefaction_plots/average_plots $alpha_rarefaction_plots.files_path
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34 ]]></command>
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35 <inputs>
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36 <param argument="--otu_table_fp" type="data" format="tabular,txt,tsv,biom" label="OTU table"/>
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37 <param argument="--mapping_fp" type="data" format="tabular,txt,tsv" label="Mapping file"/>
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38 <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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39 <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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40 <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="True" label="Run in parallel where available?"/>
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41 <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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42 <param argument="--min_rare_depth" type="integer" value="10" label="Lower limit of rarefaction depths"/>
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43 <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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44 <param argument="--retain_intermediate_files" type="boolean" truevalue="--retain_intermediate_files" falsevalue="" checked="True" label="Retain intermediate files?"/>
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45 </inputs>
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46 <outputs>
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47 <data name="alpha_rarefaction_plots" format="html" label="${tool.name} on ${on_string}: Alpha rarefaction plots"/>
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48 <collection name="alpha_diversity" type="list" label="${tool.name} on ${on_string}: Alpha diversity information">
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49 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" directory="alpha_rarefaction/alpha_div_collated/"/>
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50 </collection>
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51 <collection name="rarefaction" type="list" label="${tool.name} on ${on_string}: Rarefied OTU tables">
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52 <discover_datasets pattern="rarefaction_(?P&lt;designation&gt;.+)\.biom" directory="alpha_rarefaction/rarefaction/"/>
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53 <filter>retain_intermediate_files!=''</filter>
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54 </collection>
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55 <collection name="alpha_div" type="list" label="${tool.name} on ${on_string}: Alpha diversity results">
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56 <discover_datasets pattern="alpha_rarefaction_(?P&lt;designation&gt;.+)\.txt" directory="alpha_rarefaction/alpha_div/"/>
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57 <filter>retain_intermediate_files!=''</filter>
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58 </collection>
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59 </outputs>
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60 <tests>
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61 <test>
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62 <param name="otu_table_fp" value="alpha_rarefaction/otu_table.biom"/>
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63 <param name="mapping_fp" value="alpha_rarefaction/mapping_file.txt"/>
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64 <param name="num_steps" value="2"/>
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65 <param name="parallel" value=""/>
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66 <param name="tree_fp" value="alpha_rarefaction/rep_set.tre"/>
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67 <param name="min_rare_depth" value="10"/>
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68 <param name="max_rare_depth" value="50"/>
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69 <param name="retain_intermediate_files" value="--retain_intermediate_files"/>
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70 <output name="alpha_rarefaction_plots">
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71 <assert_contents>
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72 <has_text text="Control_mouse_I.D._354" />
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73 </assert_contents>
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74 </output>
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75 <output_collection name="alpha_diversity" type="list" count="3">
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76 <element name="chao1">
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77 <assert_contents>
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78 <has_text text="alpha_rarefaction_10_0" />
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79 <has_text text="alpha_rarefaction_30_5" />
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80 <has_text text="alpha_rarefaction_50_9" />
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81 </assert_contents>
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82 </element>
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83 <element name="observed_otus">
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84 <assert_contents>
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85 <has_text text="alpha_rarefaction_10_0" />
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86 <has_text text="alpha_rarefaction_30_5" />
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87 <has_text text="alpha_rarefaction_50_9" />
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88 </assert_contents>
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89 </element>
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90 <element name="PD_whole_tree">
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91 <assert_contents>
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92 <has_text text="alpha_rarefaction_10_0" />
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93 <has_text text="alpha_rarefaction_30_5" />
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94 <has_text text="alpha_rarefaction_50_9" />
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95 </assert_contents>
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96 </element>
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97 </output_collection>
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98 <output_collection name="rarefaction" type="list" count="30">
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99 <element name="10_0">
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100 <assert_contents>
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101 <has_text text="PC.636" />
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102 <has_text text="PC.354" />
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103 <has_text text="PC.634" />
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104 </assert_contents>
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105 </element>
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106 <element name="30_6">
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107 <assert_contents>
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108 <has_text text="PC.636" />
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109 <has_text text="PC.354" />
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110 <has_text text="PC.634" />
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111 </assert_contents>
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112 </element>
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113 <element name="50_9">
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114 <assert_contents>
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115 <has_text text="PC.636" />
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116 <has_text text="PC.354" />
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117 <has_text text="PC.634" />
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118 </assert_contents>
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119 </element>
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120 </output_collection>
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121 <output_collection name="alpha_div" type="list" count="30">
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122 <element name="10_0">
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123 <assert_contents>
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124 <has_text text="PC.636" />
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125 <has_text text="PC.354" />
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126 <has_text text="PC.634" />
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127 </assert_contents>
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128 </element>
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129 <element name="30_6">
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130 <assert_contents>
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131 <has_text text="PC.636" />
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132 <has_text text="PC.354" />
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133 <has_text text="PC.634" />
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134 </assert_contents>
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135 </element>
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136 <element name="50_9">
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137 <assert_contents>
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138 <has_text text="PC.636" />
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139 <has_text text="PC.354" />
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140 <has_text text="PC.634" />
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141 </assert_contents>
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142 </element>
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143 </output_collection>
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144 </test>
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145 </tests>
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146 <help><![CDATA[
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147 **What it does**
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148
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149 This script performs alpha rarefaction in several steps:
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150
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151 - Generation of rarefied OTU tables
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152 - Computation of alpha diversity metrics for each rarefied OTU table
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153 - Concatenation of alpha diversity results
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154 - Generation of alpha rarefaction plots
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155
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156 More information about this tool is available on
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157 `QIIME documentation <http://qiime.org/scripts/alpha_rarefaction.html>`_.
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158 ]]></help>
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159 <citations>
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160 <expand macro="citations"/>
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161 </citations>
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162 </tool>