annotate aldex2.xml @ 0:f4d0bd4b4d6d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
author iuc
date Wed, 29 Jun 2022 07:36:45 +0000
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children 75214276e2b7
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f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
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1 <tool id="aldex2" name="ALDEx2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>differential abundance analysis</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="biotools"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ## Enable building the conditions_vector.
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
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10 #set group_names = []
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11 #set num_cols = []
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12 #for $condition_items in $conditions:
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13 $group_names.append(str($condition_items.group_name))
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
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14 $num_cols.append(str($condition_items.num_cols))
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15 #end for
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16 #set group_names = ','.join($group_names)
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
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17 #set num_cols = ','.join($num_cols)
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18
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19 #if str($analysis_type_cond.analysis_type) == 'aldex_corr':
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
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20 ## Enable building the cond_var (a continuous numeric vector).
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
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21 #set group_nums = []
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22 #set num_cols_in_groups = []
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23 #for $cont_var_items in $analysis_type_cond.cont_var:
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24 $group_nums.append(str($cont_var_items.group_num))
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25 $num_cols_in_groups.append(str($cont_var_items.num_cols_in_group))
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26 #end for
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27 #set group_nums = ','.join($group_nums)
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28 #set num_cols_in_groups = ','.join($num_cols_in_groups)
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29 #end if
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30
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31 Rscript '${__tool_directory__}/aldex2.R'
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
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32 --reads '$reads'
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33 --group_names '$group_names'
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34 --num_cols '$num_cols'
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35 --num_mc_samples $num_mc_samples
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36 --denom '$denom'
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37 --analysis_type '$analysis_type_cond.analysis_type'
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38 #if str($analysis_type_cond.analysis_type) == 'aldex':
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39 --aldex_test '$analysis_type_cond.aldex_test'
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40 --effect '$analysis_type_cond.effect'
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41 --include_sample_summary '$analysis_type_cond.include_sample_summary'
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42 --iterate '$analysis_type_cond.iterate'
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43 #else if str($analysis_type_cond.analysis_type) == 'aldex_corr':
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44 --group_nums '$group_nums'
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45 --num_cols_in_groups '$num_cols_in_groups'
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46 #else if str($analysis_type_cond.analysis_type) == 'aldex_effect':
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
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47 --include_sample_summary '$analysis_type_cond.include_sample_summary'
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48 #else if str($analysis_type_cond.analysis_type) == 'aldex_plot':
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49 --aldex_test '$analysis_type_cond.aldex_test'
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50 --effect '$analysis_type_cond.effect'
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51 --include_sample_summary '$analysis_type_cond.include_sample_summary'
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52 --iterate '$analysis_type_cond.iterate'
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53 --plot_type '$analysis_type_cond.plot_type'
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54 --plot_test '$analysis_type_cond.plot_test'
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55 --cutoff_pval $analysis_type_cond.cutoff_pval
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56 --cutoff_effect $analysis_type_cond.cutoff_effect
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57 #if str($analysis_type_cond.xlab) != '':
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58 --xlab '$analysis_type_cond.xlab'
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59 #end if
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60 #if str($analysis_type_cond.ylab) != '':
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61 --ylab '$analysis_type_cond.ylab'
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62 #end if
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63 #else if str($analysis_type_cond.analysis_type) == 'aldex_plot_feature':
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64 --feature_name '$analysis_type_cond.feature_name'
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65 #else if str($analysis_type_cond.analysis_type) == 'aldex_ttest':
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66 --paired_test '$analysis_type_cond.paired_test'
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67 --hist_plot '$analysis_type_cond.hist_plot'
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68 #end if
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69 #if str($analysis_type_cond.analysis_type) == 'aldex':
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70 --output '$output_aldex'
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71 #else if str($analysis_type_cond.analysis_type) == 'aldex_corr':
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72 --output '$output_aldex_corr'
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73 #else if str($analysis_type_cond.analysis_type) == 'aldex_effect':
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74 --output '$output_aldex_effect'
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75 #else if str($analysis_type_cond.analysis_type) == 'aldex_expected_distance':
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76 --output '$output_aldex_expected_distance'
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77 #else if str($analysis_type_cond.analysis_type) == 'aldex_kw':
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78 --output '$output_aldex_kw'
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79 #else if str($analysis_type_cond.analysis_type) == 'aldex_plot':
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80 --output '$output_aldex_plot'
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81 #else if str($analysis_type_cond.analysis_type) == 'aldex_plot_feature':
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82 --output '$output_aldex_plot_feature'
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83 #else if str($analysis_type_cond.analysis_type) == 'aldex_ttest':
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84 --output '$output_aldex_ttest'
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85 #if str($analysis_type_cond.hist_plot) == 'true':
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86 && mv 'Rplots.pdf' '$output_aldex_ttest_plot'
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87 #end if
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88 #end if
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89 ]]></command>
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90 <inputs>
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91 <param argument="--reads" type="data" format="tabular" label="Reads table file" help="Rows contain genes and columns contain sequencing read counts"/>
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92 <repeat name="conditions" title="Comparison group" min="1">
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93 <param name="group_name" type="text" value="Grp1" label="Group name" help="Specify a group label and the number of sequencing read count columns associated with it">
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94 <validator type="empty_field"/>
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95 <expand macro="sanitize_query" validinitial="string.ascii_letters,string.punctuation"/>
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96 </param>
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97 <param name="num_cols" type="integer" min="1" value="1" label="Number of columns in group"/>
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98 </repeat>
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99 <param argument="--num_mc_samples" type="integer" min="1" value="128" label="Number of Monte Carlo samples to use when estimating the underlying distributions"/>
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100 <param argument="--denom" type="select" label="Select features to retain as the denominator for the Geometric Mean calculation">
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101 <option value="all" selected="true">All features</option>
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102 <option value="median">Median abundance of all features</option>
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103 <option value="iqlr">Features that are between the first and third quartile of the variance of the clr values across all samples</option>
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104 <option value="zero">Non-zero features in each group as the denominator</option>
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105 <option value="lvha">features that have low variance and high relative abundance</option>
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106 </param>
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107 <conditional name="analysis_type_cond">
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108 <param name="analysis_type" type="select" label="Select the analysis to be performed">
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109 <option value="aldex" selected="true">Compute an ALDEx2 object (aldex)</option>
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110 <option value="aldex_corr">Calculate correlation with a continuous variable (aldex.corr)</option>
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111 <option value="aldex_effect">Calculate effect sizes and differences between conditions (aldex.effect)</option>
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112 <option value="aldex_expected_distance">Calculate the expected values of distances between samples (aldex.expectedDistance)</option>
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113 <option value="aldex_kw">Calculate the Kruskal-Wallis test and glm ANOVA statistics (aldex.kw)</option>
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114 <option value="aldex_plot">Plot an ALDEx2 object (aldex.plot)</option>
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115 <option value="aldex_plot_feature">Show dispersion of the expected values returned by aldex.effect (aldex.plotFeature)</option>
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116 <option value="aldex_ttest">Calculate Welch’s t-test and Wilcoxon test statistics (aldex.ttest)</option>
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117 </param>
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118 <when value="aldex">
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119 <expand macro="aldex_test_param"/>
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120 <expand macro="effect_param"/>
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121 <expand macro="include_sample_summary_param"/>
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122 <expand macro="iterate_param"/>
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123 </when>
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124 <when value="aldex_corr">
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125 <repeat name="cont_var" title="Group number" min="1">
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126 <param name="group_num" type="integer" min="1" value="1" label="Group number" help="Specify a group number and the number of columns from the Reads table file associated with the group"/>
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127 <param name="num_cols_in_group" type="integer" min="1" value="1" label="Number of columns in group"/>
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128 </repeat>
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129 </when>
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130 <when value="aldex_effect">
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131 <expand macro="include_sample_summary_param"/>
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132 </when>
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133 <when value="aldex_expected_distance"/>
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134 <when value="aldex_kw"/>
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135 <when value="aldex_plot">
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136 <expand macro="aldex_test_param"/>
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137 <expand macro="effect_param"/>
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138 <expand macro="include_sample_summary_param"/>
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139 <expand macro="iterate_param"/>
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140 <param name="plot_type" type="select" label="Select the plot type">
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141 <option value="MA" selected="true">A Bland-Altman style plot</option>
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142 <option value="MW">A difference between to a variance within plot</option>
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143 </param>
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144 <param name="plot_test" type="select" label="Select the method of calculating significance">
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145 <option value="welch" selected="true">Welch’s t test</option>
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146 <option value="wilcox">Wilcox rank test</option>
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147 <option value="kruskal">Kruskal-Wallace test</option>
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148 </param>
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149 <param name="cutoff_pval" type="float" value="0.1" min="0" label="Benjamini-Hochberg fdr cutoff"/>
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150 <param name="cutoff_effect" type="integer" value="1" min="0" label="Effect size cutoff for plotting"/>
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151 <param name="xlab" type="text" value="" optional="true" label="x-label for the plot">
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152 <expand macro="sanitize_query" validinitial="string.ascii_letters,string.punctuation"/>
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153 </param>
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154 <param name="ylab" type="text" value="" optional="true" label="y-label for the plot">
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155 <expand macro="sanitize_query" validinitial="string.ascii_letters,string.punctuation"/>
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156 </param>
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157 </when>
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158 <when value="aldex_plot_feature">
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159 <param name="feature_name" type="text" value="" label="Name of the feature from the input data to be plotted">
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160 <expand macro="sanitize_query" validinitial="string.ascii_letters,string.punctuation"/>
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161 </param>
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162 </when>
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163 <when value="aldex_ttest">
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164 <param argument="--paired_test" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Calculate effect size for paired samples?"/>
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165 <param argument="--hist_plot" type="select" label="Plot a histogram of p-values for the first Dirichlet Monte Carlo instance?">
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166 <option value="false" selected="true">No</option>
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167 <option value="true">Yes</option>
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168 </param>
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169 </when>
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170 </conditional>
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171 </inputs>
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172 <outputs>
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173 <data name="output_aldex" format="tabular" label="${tool.name} on ${on_string}: (aldex)">
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174 <filter>analysis_type_cond['analysis_type'] == 'aldex'</filter>
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175 </data>
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176 <data name="output_aldex_corr" format="tabular" label="${tool.name} on ${on_string}: (aldex.corr)">
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177 <filter>analysis_type_cond['analysis_type'] == 'aldex_corr'</filter>
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178 </data>
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179 <data name="output_aldex_effect" format="tabular" label="${tool.name} on ${on_string}: (aldex.effect)">
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180 <filter>analysis_type_cond['analysis_type'] == 'aldex_effect'</filter>
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181 </data>
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182 <data name="output_aldex_expected_distance" format="png" label="${tool.name} on ${on_string}: (aldex.expectedDistance)">
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183 <filter>analysis_type_cond['analysis_type'] == 'aldex_expected_distance'</filter>
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184 </data>
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185 <data name="output_aldex_kw" format="tabular" label="${tool.name} on ${on_string}: (aldex.kw)">
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186 <filter>analysis_type_cond['analysis_type'] == 'aldex_kw'</filter>
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187 </data>
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188 <data name="output_aldex_plot" format="png" label="${tool.name} on ${on_string}: (aldex.plot)">
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189 <filter>analysis_type_cond['analysis_type'] == 'aldex_plot'</filter>
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190 </data>
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191 <data name="output_aldex_plot_feature" format="png" label="${tool.name} on ${on_string}: (aldex.plotFeature)">
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192 <filter>analysis_type_cond['analysis_type'] == 'aldex_plot_feature'</filter>
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193 </data>
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194 <data name="output_aldex_ttest" format="tabular" label="${tool.name} on ${on_string}: (aldex.ttest)">
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195 <filter>analysis_type_cond['analysis_type'] == 'aldex_ttest'</filter>
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196 </data>
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197 <data name="output_aldex_ttest_plot" format="pdf" label="${tool.name} on ${on_string}: (aldex.ttest hist plot)">
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198 <filter>analysis_type_cond['analysis_type'] == 'aldex_ttest' and analysis_type_cond['hist_plot'] == 'true'</filter>
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199 </data>
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200 </outputs>
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201 <tests>
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202 <test expect_num_outputs="1">
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203 <param name="reads" value="reads.tabular" ftype="tabular"/>
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204 <repeat name="conditions">
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205 <param name="group_name" value="NS"/>
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206 <param name="num_cols" value="7"/>
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207 </repeat>
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208 <repeat name="conditions">
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209 <param name="group_name" value="S"/>
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210 <param name="num_cols" value="7"/>
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211 </repeat>
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212 <output name="output_aldex" ftype="tabular">
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213 <assert_contents>
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214 <has_text text="rab.all"/>
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215 <has_size value="39906" delta="100"/>
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216 </assert_contents>
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217 </output>
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218 </test>
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219 <test expect_num_outputs="1">
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220 <param name="reads" value="reads.tabular" ftype="tabular"/>
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221 <repeat name="conditions">
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222 <param name="group_name" value="NS"/>
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223 <param name="num_cols" value="7"/>
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224 </repeat>
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225 <repeat name="conditions">
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226 <param name="group_name" value="S"/>
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227 <param name="num_cols" value="7"/>
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228 </repeat>
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229 <param name="denom" value="zero"/>
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230 <output name="output_aldex" ftype="tabular">
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231 <assert_contents>
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232 <has_text text="rab.all"/>
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233 <has_size value="39908" delta="100"/>
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234 </assert_contents>
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235 </output>
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236 </test>
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237 <test expect_num_outputs="1">
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238 <param name="reads" value="reads.tabular" ftype="tabular"/>
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239 <repeat name="conditions">
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240 <param name="group_name" value="NS"/>
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241 <param name="num_cols" value="7"/>
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242 </repeat>
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243 <repeat name="conditions">
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244 <param name="group_name" value="S"/>
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245 <param name="num_cols" value="7"/>
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246 </repeat>
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247 <param name="effect" value="false"/>
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248 <param name="include_sample_summary" value="true"/>
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249 <param name="iterate" value="true"/>
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250 <output name="output_aldex" ftype="tabular">
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251 <assert_contents>
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252 <has_text text="we.ep"/>
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253 <has_size value="14595" delta="100"/>
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254 </assert_contents>
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255 </output>
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256 </test>
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257 <test expect_num_outputs="1">
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258 <param name="reads" value="reads.tabular" ftype="tabular"/>
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259 <repeat name="conditions">
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260 <param name="group_name" value="NS"/>
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261 <param name="num_cols" value="7"/>
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262 </repeat>
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263 <repeat name="conditions">
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264 <param name="group_name" value="S"/>
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265 <param name="num_cols" value="7"/>
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266 </repeat>
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267 <param name="aldex_test" value="kw"/>
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268 <output name="output_aldex" ftype="tabular">
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269 <assert_contents>
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270 <has_text text="kw.ep"/>
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271 <has_size value="14615" delta="100"/>
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272 </assert_contents>
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273 </output>
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274 </test>
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275 <test expect_num_outputs="1">
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276 <param name="reads" value="reads.tabular" ftype="tabular"/>
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277 <repeat name="conditions">
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278 <param name="group_name" value="NS"/>
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279 <param name="num_cols" value="7"/>
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280 </repeat>
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281 <repeat name="conditions">
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282 <param name="group_name" value="S"/>
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283 <param name="num_cols" value="7"/>
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284 </repeat>
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285 <param name="analysis_type" value="aldex_corr"/>
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286 <repeat name="cont_var">
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287 <param name="group_num" value="1"/>
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288 <param name="num_cols_in_group" value="7"/>
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289 </repeat>
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290 <repeat name="cont_var">
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iuc
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291 <param name="group_num" value="2"/>
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iuc
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292 <param name="num_cols_in_group" value="7"/>
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293 </repeat>
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294 <output name="output_aldex_corr" ftype="tabular">
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295 <assert_contents>
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296 <has_text text="pearson.ecor"/>
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297 <has_size value="33232" delta="100"/>
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298 </assert_contents>
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299 </output>
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300 </test>
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iuc
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301 <test expect_num_outputs="1">
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302 <param name="reads" value="reads.tabular" ftype="tabular"/>
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iuc
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303 <repeat name="conditions">
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iuc
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304 <param name="group_name" value="NS"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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305 <param name="num_cols" value="7"/>
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306 </repeat>
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iuc
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diff changeset
307 <repeat name="conditions">
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iuc
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308 <param name="group_name" value="S"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
309 <param name="num_cols" value="7"/>
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310 </repeat>
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311 <param name="analysis_type" value="aldex_effect"/>
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iuc
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312 <output name="output_aldex_effect" ftype="tabular">
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313 <assert_contents>
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314 <has_text text="rab.all"/>
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315 <has_size value="25268" delta="100"/>
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316 </assert_contents>
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317 </output>
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318 </test>
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319 <test expect_num_outputs="1">
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320 <param name="reads" value="reads.tabular" ftype="tabular"/>
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321 <repeat name="conditions">
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322 <param name="group_name" value="NS"/>
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323 <param name="num_cols" value="7"/>
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324 </repeat>
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diff changeset
325 <repeat name="conditions">
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iuc
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diff changeset
326 <param name="group_name" value="S"/>
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iuc
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327 <param name="num_cols" value="7"/>
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328 </repeat>
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329 <param name="analysis_type" value="aldex_expected_distance"/>
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330 <output name="output_aldex_expected_distance" ftype="png">
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331 <assert_contents>
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332 <has_size value="70183" delta="2000"/>
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333 </assert_contents>
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334 </output>
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335 </test>
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336 <test expect_num_outputs="1">
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337 <param name="reads" value="reads.tabular" ftype="tabular"/>
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iuc
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338 <repeat name="conditions">
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iuc
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339 <param name="group_name" value="NS"/>
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340 <param name="num_cols" value="7"/>
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341 </repeat>
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iuc
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diff changeset
342 <repeat name="conditions">
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iuc
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diff changeset
343 <param name="group_name" value="S"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
344 <param name="num_cols" value="7"/>
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345 </repeat>
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346 <param name="analysis_type" value="aldex_kw"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
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347 <output name="output_aldex_kw" ftype="tabular">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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348 <assert_contents>
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iuc
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diff changeset
349 <has_text text="kw.ep"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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350 <has_size value="14623" delta="100"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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351 </assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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352 </output>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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353 </test>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
354 <test expect_num_outputs="1">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
355 <param name="reads" value="reads.tabular" ftype="tabular"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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356 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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357 <param name="group_name" value="NS"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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358 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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359 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
360 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
361 <param name="group_name" value="S"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
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362 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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363 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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364 <param name="analysis_type" value="aldex_plot"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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365 <output name="output_aldex_plot" ftype="png">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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366 <assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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367 <has_size value="19064" delta="500"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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368 </assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
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369 </output>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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370 </test>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
371 <test expect_num_outputs="1">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
372 <param name="reads" value="reads.tabular" ftype="tabular"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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373 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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374 <param name="group_name" value="NS"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
375 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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376 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
377 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
378 <param name="group_name" value="S"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
379 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
380 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
381 <param name="analysis_type" value="aldex_plot_feature"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
382 <param name="feature_name" value="A:D:A:E"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
383 <output name="output_aldex_plot_feature" ftype="png">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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384 <assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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385 <has_size value="30772" delta="2000"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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386 </assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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387 </output>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
388 </test>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
389 <test expect_num_outputs="1">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
390 <param name="reads" value="reads.tabular" ftype="tabular"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
391 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
392 <param name="group_name" value="NS"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
393 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
394 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
395 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
396 <param name="group_name" value="S"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
397 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
398 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
399 <param name="analysis_type" value="aldex_ttest"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
400 <output name="output_aldex_ttest" ftype="tabular">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
401 <assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
402 <has_text text="we.ep"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
403 <has_size value="14596" delta="100"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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404 </assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
405 </output>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
406 </test>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
407 <test expect_num_outputs="2">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
408 <param name="reads" value="reads.tabular" ftype="tabular"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
409 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
410 <param name="group_name" value="NS"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
411 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
412 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
413 <repeat name="conditions">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
414 <param name="group_name" value="S"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
415 <param name="num_cols" value="7"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
416 </repeat>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
417 <param name="analysis_type" value="aldex_ttest"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
418 <param name="paired_test" value="true"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
419 <param name="hist_plot" value="true"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
420 <output name="output_aldex_ttest" ftype="tabular">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
421 <assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
422 <has_text text="we.ep"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
423 <has_size value="13822" delta="100"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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424 </assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
425 </output>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
426 <output name="output_aldex_ttest_plot" ftype="pdf">
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
427 <assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
428 <has_text text="%PDF"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
429 <has_size value="7331" delta="100"/>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
430 </assert_contents>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
431 </output>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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diff changeset
432 </test>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
433 </tests>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
434 <help>
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
parents:
diff changeset
435 **What it does**
f4d0bd4b4d6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 commit b99f09cf03f075a6881d192b0f1233233289fa60
iuc
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436
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437 Performs a differential abundance analysis for the comparison of two or more conditions (e.g., single-organism
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438 and meta-RNA-seq high-throughput sequencing assays, or of selected and unselected values from in-vitro sequence
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439 selections). This tool generates Monte Carlo samples of the Dirichlet distribution for each sample, converts
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440 each instance using a log-ratio transform, then returns test results for two sample (Welch’s t, Wilcoxon) or
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441 multi-sample (glm, Kruskal-Wallace) tests. The tool also estimates effect size for two sample analyses.
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442
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443 **Options**
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444
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445 * **Reads table file** - a tabular file with unique names for all rows and columns. Rows should contain genes and columns should contain sequencing read counts (i.e., sample vectors). Rows with 0 reads in each sample are deleted prior to analysis.
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446 * **Define the comparison groups describing the reads data structure** - Specify a group label and the number of sequencing read count columns associated with it. The total number of columns must be equal to the number of numeric columns in the selected Reads table file.
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447 * **Number of Monte Carlo samples to use** - the number of Monte Carlo samples to use when estimating the underlying distributions. Since we are estimating central tendencies, 128 is usually sufficient.
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448 * **Select features to retain as the denominator for the Geometric Mean calculation** - indicates which features to retain as the denominator for the Geometric Mean calculation.
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449 * **Select the analysis to be performed**
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450
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451 * **Compute an ALDEx2 object (aldex)** - performs log-ratio transformation and statistical testing. Specifically, this function: (a) generates Monte Carlo samples of the Dirichlet distribution for each sample, (b) converts each instance using a log-ratio transform, then (c) retcalculates the expected values for the correlation between each feature and a contin- uous variable, using data returned returned by aldex.clr and a vector of the continuous variable. Returns results of Pearson, Spearman and Kendall tests.urns test results for two sample (Welch’s t, Wilcoxon) or multi-sample (glm, Kruskal-Wallace) tests. This function also estimates effect size for two sample analyses.
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452
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453 * **Select the tests to be performed** - select the tests to be performed when crearing the ALDEx2 object.
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454 * **Calculate abundances and effect sizes** - applies only if the selected test is Welch’s t and Wilcox tests, or if tests are performed iteratively.
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455 * **Include median clr values for each sample** - specify whether to include median clr values for each sample (applies only if abundances and effect sizes are calculated).
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456 * **Perform tests iteratively** - Specify whether to iteratively perform a test. For example, this will use the results from an initial Welch’s t and Wilcox test routine to seed the reference (i.e., denominator of Geometric Mean calculation) for a second Welch’s t and Wilcox test routine.
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457
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458 * **Calculate correlation with a continuous variable (aldex.corr)** - calculates the expected values for the correlation between each feature and a continuous variable using data returned by aldex.clr and a vector of the continuous variable. Returns results of Pearson, Spearman and Kendall tests.
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459 * **Calculate effect sizes and differences between conditions (aldex.effect)** - calculates (1) the median clr abundances per sample, per condition, (2) the median differences in abundance between 2 conditions and (3) the median effect size and proportion of effect that overlaps 0.
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460 * **Calculate the expected values of distances between samples (aldex.expectedDistance)** - calculates the expected value of distances between samples using the median value of distances derived from N Monte-Carlo replicates.
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461 * **Calculate the Kruskal-Wallis test and glm ANOVA statistics (aldex.kw)** - calculates the expected values of the Kruskal-Wallis test and a glm ANOVA.
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462 * **Plot an ALDEx2 object (aldex.plot)** - generate an MW-plot or an MA-plot of the given ALDEx2 object.
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463 * **Show dispersion of the expected values returned by aldex.effect (aldex.plotFeature)** - generates density plots showing the dispersion of the expected values given in the output from aldex.effect. The expected values are shown in the plots. This is a diagnostic visualization to help determine if the expected values are trustworthy.
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464 * **Calculate Welch’s t-test and Wilcoxon test statistics (aldex.ttest)** - calculate the expected values of the Wilcoxon Rank Sum test and Welch's t-test on the data returned by aldex.clr
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465
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466 * **Calculate paired tests** - specify whether to calculate effect size for paired samples (applies only if abundances and effect sizes are calculated and the selected test is Welch’s t and Wilcox tests).
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467 * **Plot a histogram of p-values for the first Dirichlet Monte Carlo instance** - specify whether to plot a histogram of p-values for the first Dirichlet Monte Carlo instance.
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468 </help>
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469 <expand macro="citations"/>
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470 </tool>
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471