Mercurial > repos > iuc > freyja_aggregate_plot

annotate freyja_aggregate_plot.xml @ 0:0ceb9fb0f4ce draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
author iuc
date Thu, 28 Jul 2022 09:25:04 +0000
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0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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1 <tool id="freyja_aggregate_plot" name="Freyja: Aggregate and visualize"
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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2 version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
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3 profile="@PROFILE@">
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4 <description>
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5 demixed results
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6 </description>
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7 <macros>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="biotools"/>
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11 <expand macro="requirements"/>
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12 <expand macro="version"/>
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13 <command detect_errors="exit_code"><![CDATA[
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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14 #if $need_aggregation.choice == 'yes'
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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15 #set demix_dir = 'demix_outputs/'
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16 #set file_paths1 = []
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17 mkdir -p demix_outputs &&
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18 #for $input_file in $demix_file
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19 #set $file_path = $demix_dir + $input_file.element_identifier
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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20 ln -s '$input_file' '$file_path' &&
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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21 $file_paths1.append($file_path)
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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22 #end for
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23 freyja aggregate
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24 '$demix_dir'
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25 --output aggregated.tsv
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26 #if $plot_format.choice != 'none'
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27 &&
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28 #end if
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29 #end if
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30 @PLOT_AND_DASH_COMMAND@
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31 ]]></command>
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32 <inputs>
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33 <conditional name="need_aggregation">
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34 <param name="choice" type="select"
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35 label="Aggregate demixed data or provide aggregated data file?">
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36 <option value="yes">aggregate demixed data</option>
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37 <option value="no">provide aggregated data file</option>
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38 </param>
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39 <when value="yes">
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40 <param name="demix_file" type="data" format="tabular" multiple="true"
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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41 label="Lineages abundances summary file(s)" help="One file per one sample."/>
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42 </when>
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43 <when value="no">
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44 <param name="tsv_aggregated" type="data" format="tabular"
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45 label="Provide aggregated data"/>
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46 </when>
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47 </conditional>
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48 <conditional name="plot_format">
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49 <param name="choice" type="select" label="Report(s) to generate">
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50 <option value="plot">non-interactive plot</option>
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51 <option value="dash">interactive dashboard (html)</option>
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52 <option value="plot_and_dash">plot and dashboard</option>
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53 <option value="none">no plots, just aggregated data table</option>
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54 </param>
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55 <when value="plot">
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56 <conditional name="need_metadata">
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57 <param name="choice" type="select"
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58 label="Provide a sample metadata file for plotting data over time?">
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59 <option value="yes">Yes</option>
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60 <option value="no">No</option>
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61 </param>
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62 <when value="yes">
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63 <param name="csv_meta" type="data" format="csv"
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64 label="Provide time(s) metadata file"
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65 help="See info box below to learn more about the form of meta-file. Accepts only CSV (.csv) files"/>
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66 <param name="interval" type="select" label="Choose interval" display="radio"
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67 help="Used for pdf format.">
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68 <option value="MS" selected="true">month bins</option>
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69 <option value="D">day bins</option>
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70 </param>
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71 </when>
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72 <when value="no"/>
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73 </conditional>
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74 </when>
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75 <when value="dash">
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76 <param name="csv_meta" type="data" format="csv"
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77 label="Provide sample(s) metadata file"
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78 help="See info box below to learn more about the form of meta-file. Accepts only CSV (.csv) files"/>
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79 <param name="plot_title" type="text" value="" optional="true" label="Title"/>
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80 <param name="plot_intro" type="text" value="" optional="true" label="Introduction"/>
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81 </when>
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82 <when value="plot_and_dash">
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83 <param name="csv_meta" type="data" format="csv"
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84 label="Provide sample(s)/time(s) metadata file"
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85 help="See info box below to learn more about the form of meta-file. Accepts only CSV (.csv) files"/>
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86 <param name="plot_title" type="text" value="" optional="true" label="Title"
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87 help="Used for interactive dashboard."/>
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88 <param name="plot_intro" type="text" value="" optional="true" label="Introduction"
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89 help="Used for interactive dashboard."/>
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90 <param name="interval" type="select" label="Choose interval" display="radio"
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91 help="Used for pdf non-interactive plot.">
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92 <option value="MS" selected="true">month bins</option>
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93 <option value="D">day bins</option>
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94 </param>
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95 </when>
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96 <when value="none"/>
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97 </conditional>
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98 </inputs>
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99 <outputs>
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100 <!-- outputs for aggregate command -->
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101 <data name="aggregated" format="tabular"
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102 label="${tool.name} on ${on_string}: Aggregated data"
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103 from_work_dir="aggregated.tsv">
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104 <filter>need_aggregation['choice'] == 'yes'</filter>
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105 </data>
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106 <!-- outputs for dash command -->
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107 <data name="abundances_dashboard" format="html"
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108 label="${tool.name} on ${on_string}: Lineages abundances dashboard"
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109 from_work_dir="abundances_dashboard.html">
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110 <filter>plot_format['choice'] == 'dash' or plot_format['choice'] == 'plot_and_dash'
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111 </filter>
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112 </data>
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113 <!-- outputs for plot command -->
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114 <data name="abundances_plot" format="pdf"
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115 label="${tool.name} on ${on_string}: Lineages abundances plot"
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116 from_work_dir="abundances_plot.pdf">
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117 <filter>plot_format['choice'] == 'plot' or plot_format['choice'] == 'plot_and_dash'
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118 </filter>
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119 </data>
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120 </outputs>
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121 <tests>
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122 <!-- Test 01: aggregate command -->
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123 <test expect_num_outputs="1">
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124 <conditional name="need_aggregation">
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125 <param name="choice" value="yes"/>
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126 <param name="demix_file"
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127 value="abundances.tsv,abundances2.tsv,abundances3.tsv,abundances4.tsv"/>
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128 </conditional>
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129 <conditional name="plot_format">
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130 <param name="choice" value="none"/>
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131 </conditional>
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132 <output name="aggregated" ftype="tabular">
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133 <assert_contents>
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134 <has_text text="summarized"/>
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135 <has_text text="abundances"/>
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136 <has_text text="B.1.617.2"/>
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137 </assert_contents>
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138 </output>
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139 </test>
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140 <!-- Test 02: dash command -->
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141 <test expect_num_outputs="1">
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142 <conditional name="need_aggregation">
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143 <param name="choice" value="no"/>
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144 <param name="tsv_aggregated" value="bunch_of_files.tsv"/>
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145 </conditional>
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146 <conditional name="plot_format">
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147 <param name="choice" value="dash"/>
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148 <param name="csv_meta" value="csv_sample_meta.csv"/>
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149 <param name="plot_title" value="This is title"/>
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150 <param name="plot_intro" value="Local WW Dashboard"/>
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151 </conditional>
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152 <output name="abundances_dashboard" ftype="html">
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153 <assert_contents>
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154 <has_text text="Local WW Dashboard"/>
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155 </assert_contents>
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156 </output>
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157 </test>
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158 <!-- Test 03: plot command -->
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159 <test expect_num_outputs="1">
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160 <conditional name="need_aggregation">
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161 <param name="choice" value="no"/>
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162 <param name="tsv_aggregated" value="bunch_of_files.tsv"/>
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163 </conditional>
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164 <conditional name="plot_format">
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165 <param name="choice" value="plot"/>
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166 <conditional name="need_metadata">
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167 <param name="choice" value="yes"/>
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168 <param name="csv_meta" value="times_metadata.csv"/>
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169 <param name="interval" value="D"/>
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170 </conditional>
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171 </conditional>
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172 <output name="abundances_plot" ftype="pdf">
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173 <assert_contents>
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174 <has_text text="Matplotlib"/>
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175 </assert_contents>
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176 </output>
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177 </test>
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178 <!-- Test 04: aggregate and dash commands -->
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179 <test expect_num_outputs="2">
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180 <conditional name="need_aggregation">
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181 <param name="choice" value="yes"/>
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182 <param name="demix_file" value="abundances.tsv,abundances2.tsv,abundances3.tsv"/>
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183 </conditional>
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184 <conditional name="plot_format">
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185 <param name="choice" value="dash"/>
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186 <param name="csv_meta" value="csv_sample_meta2.csv"/>
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187 <param name="plot_title" value="This is title"/>
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188 <param name="plot_intro" value="Local WW Dashboard"/>
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189 </conditional>
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190 <output name="aggregated" ftype="tabular">
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191 <assert_contents>
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192 <has_text text="summarized"/>
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193 <has_text text="abundances"/>
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194 <has_text text="B.1.617.2"/>
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195 </assert_contents>
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196 </output>
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197 <output name="abundances_dashboard" ftype="html">
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198 <assert_contents>
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199 <has_text text="Local WW Dashboard"/>
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200 </assert_contents>
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201 </output>
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202 </test>
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203 <!-- Test 05: aggregate and plot commands -->
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204 <test expect_num_outputs="2">
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205 <conditional name="need_aggregation">
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206 <param name="choice" value="yes"/>
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207 <param name="demix_file" value="abundances.tsv,abundances2.tsv,abundances3.tsv"/>
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208 </conditional>
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209 <conditional name="plot_format">
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210 <param name="choice" value="plot"/>
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211 <conditional name="need_metadata">
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212 <param name="choice" value="yes"/>
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213 <param name="csv_meta" value="csv_sample_meta2.csv"/>
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214 <param name="interval" value="D"/>
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215 </conditional>
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216 </conditional>
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217 <output name="aggregated" ftype="tabular">
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218 <assert_contents>
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219 <has_text text="summarized"/>
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220 <has_text text="abundances"/>
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221 <has_text text="B.1.617.2"/>
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222 </assert_contents>
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223 </output>
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224 <output name="abundances_plot" ftype="pdf">
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225 <assert_contents>
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226 <has_text text="Matplotlib"/>
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227 </assert_contents>
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228 </output>
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229 </test>
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230 <!-- Test 06: aggregate, dash and plot commands -->
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231 <test expect_num_outputs="3">
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232 <conditional name="need_aggregation">
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233 <param name="choice" value="yes"/>
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234 <param name="demix_file" value="abundances.tsv,abundances2.tsv,abundances3.tsv"/>
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235 </conditional>
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236 <conditional name="plot_format">
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237 <param name="choice" value="plot_and_dash"/>
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238 <param name="csv_meta" value="csv_sample_meta2.csv"/>
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239 <param name="plot_title" value="This is title"/>
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240 <param name="plot_intro" value="Local WW Dashboard"/>
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241 <param name="interval" value="D"/>
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242 </conditional>
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243 <output name="aggregated" ftype="tabular">
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244 <assert_contents>
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245 <has_text text="summarized"/>
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246 <has_text text="abundances"/>
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247 <has_text text="B.1.617.2"/>
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248 </assert_contents>
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249 </output>
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250 <output name="abundances_plot" ftype="pdf">
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251 <assert_contents>
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252 <has_text text="Matplotlib"/>
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253 </assert_contents>
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254 </output>
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255 <output name="abundances_dashboard" ftype="html">
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256 <assert_contents>
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257 <has_text text="Local WW Dashboard"/>
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258 </assert_contents>
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259 </output>
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260 </test>
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261 </tests>
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262 <help><![CDATA[
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263 @HELP_HEADER@
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264
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265 Information about **freyja aggregate** method
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266 =============================================
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267
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268 Method for manipulating the "demixed" output files.
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269
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270 Outputs
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271 -------
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272
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273 This resulting aggregated data can analyzed directly as a tsv file, or can be visualized using *freyja plot* and *freyja dash*.
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274
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275 Information about **freyja plot** method
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276 ========================================
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277
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278 Method provides a fractional abundance estimate for all aggregated samples.
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279
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280 A **time(s) metadata CSV file** should have this form:
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281
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282 *Sample,sample_collection_datetime*
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283
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284 *sample_0.tsv,03/01/21*
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285
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286 *sample_1.tsv,03/03/21*
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287
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288 *sample_2.tsv,03/08/21*
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289
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290 *sample_3.tsv,03/10/21*
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291
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292 *sample_4.tsv,03/12/21*
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293
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294 *sample_5.tsv,03/14/21*
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295
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296 *sample_6.tsv,03/17/21*
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297
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298 *sample_7.tsv,03/20/21*
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299
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300 *sample_8.tsv,03/25/21*
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301
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302 *sample_9.tsv,03/30/21*
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303
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304 *sample_10.tsv,03/31/21*
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305
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306 *sample_11.tsv,04/04/21*
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307
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308
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309 Information about **freyja dash** method
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310 ========================================
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311
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312 Functionality to rapidly prepare a dashboard web page, directly from aggregated freyja output.
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313
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314 A **sample(s) metadata CSV file** should have this form:
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315
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316 *Sample,sample_collection_datetime,viral_load*
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317
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318 *sample_0.tsv,03/01/21,460326*
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319
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320 *sample_1.tsv,03/03/21,176645.1*
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321
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322 *sample_2.tsv,03/08/21,449891.7*
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323
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324 *sample_3.tsv,03/10/21,361699.5*
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325
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326 *sample_4.tsv,03/12/21,658923.9*
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327
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328 *sample_5.tsv,03/14/21,500432.8*
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329
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330 *sample_6.tsv,03/17/21,791406.4*
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331
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332 *sample_7.tsv,03/20/21,628119.9*
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333
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334 *sample_8.tsv,03/25/21,810673.9*
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335
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336 *sample_9.tsv,03/30/21,1263564.4*
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337
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338 *sample_10.tsv,03/31/21,1627556.3*
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339
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340 *sample_11.tsv,04/04/21,1528006.4*
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341
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342
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343 ]]></help>
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344 <expand macro="citations"/>
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345 </tool>