Mercurial > repos > iuc > freyja_aggregate_plot

annotate freyja_aggregate_plot.xml @ 1:1f89eeba299a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
author iuc
date Fri, 07 Jul 2023 05:51:06 +0000
parents 0ceb9fb0f4ce
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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"
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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[
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14 #if $need_aggregation.choice == 'yes'
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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 + $input_file.element_identifier
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20 ln -s '$input_file' '$file_path' &&
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21 $file_paths1.append($file_path)
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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"
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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>
1
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74 <expand macro="plot_lineages"/>
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75 <expand macro="plot_mincov"/>
0
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76 </when>
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77 <when value="dash">
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78 <param name="csv_meta" type="data" format="csv"
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79 label="Provide sample(s) metadata file"
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80 help="See info box below to learn more about the form of meta-file. Accepts only CSV (.csv) files"/>
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81 <param name="plot_title" type="text" value="" optional="true" label="Title"/>
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82 <param name="plot_intro" type="text" value="" optional="true" label="Introduction"/>
1
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83 <expand macro="plot_mincov"/>
0
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84 </when>
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85 <when value="plot_and_dash">
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86 <param name="csv_meta" type="data" format="csv"
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87 label="Provide sample(s)/time(s) metadata file"
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88 help="See info box below to learn more about the form of meta-file. Accepts only CSV (.csv) files"/>
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89 <param name="plot_title" type="text" value="" optional="true" label="Title"
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90 help="Used for interactive dashboard."/>
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91 <param name="plot_intro" type="text" value="" optional="true" label="Introduction"
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92 help="Used for interactive dashboard."/>
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93 <param name="interval" type="select" label="Choose interval" display="radio"
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94 help="Used for pdf non-interactive plot.">
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95 <option value="MS" selected="true">month bins</option>
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96 <option value="D">day bins</option>
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97 </param>
1
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98 <expand macro="plot_lineages"/>
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99 <expand macro="plot_mincov"/>
0
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100 </when>
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101 <when value="none"/>
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102 </conditional>
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103 </inputs>
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104 <outputs>
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105 <!-- outputs for aggregate command -->
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106 <data name="aggregated" format="tabular"
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107 label="${tool.name} on ${on_string}: Aggregated data"
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108 from_work_dir="aggregated.tsv">
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109 <filter>need_aggregation['choice'] == 'yes'</filter>
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110 </data>
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111 <!-- outputs for dash command -->
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112 <data name="abundances_dashboard" format="html"
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113 label="${tool.name} on ${on_string}: Lineages abundances dashboard"
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114 from_work_dir="abundances_dashboard.html">
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115 <filter>plot_format['choice'] == 'dash' or plot_format['choice'] == 'plot_and_dash'
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116 </filter>
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117 </data>
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118 <!-- outputs for plot command -->
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119 <data name="abundances_plot" format="pdf"
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120 label="${tool.name} on ${on_string}: Lineages abundances plot"
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121 from_work_dir="abundances_plot.pdf">
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122 <filter>plot_format['choice'] == 'plot' or plot_format['choice'] == 'plot_and_dash'
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123 </filter>
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124 </data>
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125 </outputs>
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126 <tests>
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127 <!-- Test 01: aggregate command -->
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128 <test expect_num_outputs="1">
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129 <conditional name="need_aggregation">
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130 <param name="choice" value="yes"/>
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131 <param name="demix_file"
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132 value="abundances.tsv,abundances2.tsv,abundances3.tsv,abundances4.tsv"/>
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133 </conditional>
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134 <conditional name="plot_format">
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135 <param name="choice" value="none"/>
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136 </conditional>
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137 <output name="aggregated" ftype="tabular">
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138 <assert_contents>
1
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139 <has_n_columns n="6" />
0
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140 <has_text text="summarized"/>
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141 <has_text text="abundances"/>
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142 <has_text text="B.1.617.2"/>
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143 </assert_contents>
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144 </output>
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145 </test>
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146 <!-- Test 02: dash command -->
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147 <test expect_num_outputs="1">
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148 <conditional name="need_aggregation">
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149 <param name="choice" value="no"/>
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150 <param name="tsv_aggregated" value="bunch_of_files.tsv"/>
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151 </conditional>
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152 <conditional name="plot_format">
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153 <param name="choice" value="dash"/>
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154 <param name="csv_meta" value="csv_sample_meta.csv"/>
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155 <param name="plot_title" value="This is title"/>
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156 <param name="plot_intro" value="Local WW Dashboard"/>
1
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157 <param name="mincov" value="75"/>
0
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158 </conditional>
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159 <output name="abundances_dashboard" ftype="html">
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160 <assert_contents>
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161 <has_text text="Local WW Dashboard"/>
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162 </assert_contents>
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163 </output>
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164 </test>
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165 <!-- Test 03: plot command -->
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166 <test expect_num_outputs="1">
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167 <conditional name="need_aggregation">
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168 <param name="choice" value="no"/>
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169 <param name="tsv_aggregated" value="bunch_of_files.tsv"/>
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170 </conditional>
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171 <conditional name="plot_format">
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172 <param name="choice" value="plot"/>
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173 <conditional name="need_metadata">
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174 <param name="choice" value="yes"/>
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175 <param name="csv_meta" value="times_metadata.csv"/>
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176 <param name="interval" value="D"/>
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177 </conditional>
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178 </conditional>
1
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179 <param name="lineages" value="true"/>
0
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180 <output name="abundances_plot" ftype="pdf">
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181 <assert_contents>
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182 <has_text text="Matplotlib"/>
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183 </assert_contents>
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184 </output>
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185 </test>
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186 <!-- Test 04: aggregate and dash commands -->
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187 <test expect_num_outputs="2">
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188 <conditional name="need_aggregation">
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189 <param name="choice" value="yes"/>
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190 <param name="demix_file" value="abundances.tsv,abundances2.tsv,abundances3.tsv"/>
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191 </conditional>
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192 <conditional name="plot_format">
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193 <param name="choice" value="dash"/>
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194 <param name="csv_meta" value="csv_sample_meta2.csv"/>
1
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195 <param name="plot_title" value="Title"/>
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196 <param name="plot_intro" value="Dashboard"/>
0
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197 </conditional>
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198 <output name="aggregated" ftype="tabular">
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199 <assert_contents>
1
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200 <has_n_columns n="6" />
0
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201 <has_text text="summarized"/>
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202 </assert_contents>
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203 </output>
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204 <output name="abundances_dashboard" ftype="html">
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205 <assert_contents>
1
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206 <has_text text="Dashboard"/>
0
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207 </assert_contents>
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208 </output>
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209 </test>
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210 <!-- Test 05: aggregate and plot commands -->
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211 <test expect_num_outputs="2">
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212 <conditional name="need_aggregation">
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213 <param name="choice" value="yes"/>
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214 <param name="demix_file" value="abundances.tsv,abundances2.tsv,abundances3.tsv"/>
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215 </conditional>
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216 <conditional name="plot_format">
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217 <param name="choice" value="plot"/>
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218 <conditional name="need_metadata">
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219 <param name="choice" value="yes"/>
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220 <param name="csv_meta" value="csv_sample_meta2.csv"/>
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221 <param name="interval" value="D"/>
0ceb9fb0f4ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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222 </conditional>
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223 </conditional>
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224 <output name="aggregated" ftype="tabular">
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225 <assert_contents>
1
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226 <has_n_columns n="6" />
0
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227 <has_text text="summarized"/>
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228 <has_text text="abundances"/>
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229 <has_text text="B.1.617.2"/>
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230 </assert_contents>
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231 </output>
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232 <output name="abundances_plot" ftype="pdf">
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233 <assert_contents>
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234 <has_text text="Matplotlib"/>
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235 </assert_contents>
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236 </output>
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237 </test>
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238 <!-- Test 06: aggregate, dash and plot commands -->
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239 <test expect_num_outputs="3">
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240 <conditional name="need_aggregation">
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241 <param name="choice" value="yes"/>
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242 <param name="demix_file" value="abundances.tsv,abundances2.tsv,abundances3.tsv"/>
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243 </conditional>
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244 <conditional name="plot_format">
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245 <param name="choice" value="plot_and_dash"/>
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246 <param name="csv_meta" value="csv_sample_meta2.csv"/>
1
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247 <param name="plot_title" value="Title"/>
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diff changeset
248 <param name="plot_intro" value="Dashboard"/>
0
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249 <param name="interval" value="D"/>
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250 </conditional>
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251 <output name="aggregated" ftype="tabular">
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252 <assert_contents>
1
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253 <has_n_columns n="6" />
0
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254 <has_text text="summarized"/>
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255 </assert_contents>
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256 </output>
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257 <output name="abundances_plot" ftype="pdf">
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258 <assert_contents>
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259 <has_text text="Matplotlib"/>
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260 </assert_contents>
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diff changeset
261 </output>
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262 <output name="abundances_dashboard" ftype="html">
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263 <assert_contents>
1
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parents: 0
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264 <has_text text="Dash"/>
0
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265 </assert_contents>
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266 </output>
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267 </test>
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268 </tests>
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269 <help><![CDATA[
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270 @HELP_HEADER@
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271
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272 Information about **freyja aggregate** method
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273 =============================================
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274
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275 Method for manipulating the "demixed" output files.
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276
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277 Outputs
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278 -------
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279
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280 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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281
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282 Information about **freyja plot** method
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283 ========================================
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284
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285 Method provides a fractional abundance estimate for all aggregated samples.
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286
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287 A **time(s) metadata CSV file** should have *Sample,sample_collection_datetime* form:
0
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288
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289 *sample_0.tsv,03/01/21*
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290
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291 *sample_1.tsv,03/03/21*
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292
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293 *sample_2.tsv,03/08/21*
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294
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295 *sample_3.tsv,03/10/21*
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296
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297 or *Sample,sample_collection_datetime,viral_load* form:
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298
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299 *sample_0.tsv,03/01/21,460326*
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300
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301 *sample_1.tsv,03/03/21,176645.1*
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302
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303 *sample_2.tsv,03/08/21,449891.7*
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304
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305 *sample_3.tsv,03/10/21,361699.5*
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306
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307
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308 Note: sample_collection_datetime can have either *MM/DD/YY* or *YYYY-MM-DD* format.
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309
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310
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311 Information about **freyja dash** method
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312 ========================================
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313
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314 Functionality to rapidly prepare a dashboard web page, directly from aggregated freyja output.
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315
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316 A **sample(s) metadata CSV file** should have this form:
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317
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318 *Sample,sample_collection_datetime,viral_load*
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319
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320 *sample_0.tsv,03/01/21,460326*
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321
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322 *sample_1.tsv,03/03/21,176645.1*
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323
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324 *sample_2.tsv,03/08/21,449891.7*
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325
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326 *sample_3.tsv,03/10/21,361699.5*
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327
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328
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329 Note: sample_collection_datetime can have either *MM/DD/YY* or *YYYY-MM-DD* format.
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330
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331
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332 ]]></help>
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333 <expand macro="citations"/>
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334 </tool>