Mercurial > repos > workflow4metabolomics > kmd_hmdb_data_plot

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ commit 7fa454b6a4268b89fe18043e8dd10f30a7b4c7ca
author workflow4metabolomics
date Tue, 29 Aug 2023 09:45:16 +0000
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59c8bad5f6bc planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ commit 7fa454b6a4268b89fe18043e8dd10f30a7b4c7ca
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1 <tool id="kmd_hmdb_data_plot" name="KMD HMDB Data Plot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
59c8bad5f6bc planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ commit 7fa454b6a4268b89fe18043e8dd10f30a7b4c7ca
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2 <description>
59c8bad5f6bc planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ commit 7fa454b6a4268b89fe18043e8dd10f30a7b4c7ca
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3 retrieves data from KMD HMDB API and produce plot and tsv file
59c8bad5f6bc planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ commit 7fa454b6a4268b89fe18043e8dd10f30a7b4c7ca
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4 </description>
59c8bad5f6bc planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ commit 7fa454b6a4268b89fe18043e8dd10f30a7b4c7ca
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5 <macros>
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6 <import>macro.xml</import>
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7 <token name="@TOOL_VERSION@">1.0.0</token>
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8 <token name="@VERSION_SUFFIX@">0</token>
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9 </macros>
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10 <edam_topics>
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11 <edam_topic>topic_0091</edam_topic>
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12 </edam_topics>
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13 <edam_operations>
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14 <edam_operation>operation_3803</edam_operation>
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15 </edam_operations>
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16 <requirements>
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17 <requirement type="package" version="3.10">python</requirement>
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18 <requirement type="package" version="2.0.3">pandas</requirement>
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19 <requirement type="package" version="5.15.0">plotly</requirement>
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20 <requirement type="package" version="1.0.1">kmd_hmdb_api_client</requirement>
59c8bad5f6bc planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ commit 7fa454b6a4268b89fe18043e8dd10f30a7b4c7ca
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21 </requirements>
59c8bad5f6bc planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ commit 7fa454b6a4268b89fe18043e8dd10f30a7b4c7ca
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22 <command detect_errors="exit_code">
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23 <![CDATA[
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24 #if "get_data" in str($what.to_do)
59c8bad5f6bc planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ commit 7fa454b6a4268b89fe18043e8dd10f30a7b4c7ca
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25 python3 '$__tool_directory__/kmd_hmdb_interrogator.py' compound
59c8bad5f6bc planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ commit 7fa454b6a4268b89fe18043e8dd10f30a7b4c7ca
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26 --mz-ratio '$what.mz_ratio'
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27 --database '$what.database'
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28 --mass-tolerance '$what.mass_tolerance'
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29 #for adduct in $what.adducts
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30 --adducts '$adduct'
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31 #end for
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32 --output-path '$output_path'
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33 #end if
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34
59c8bad5f6bc planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ commit 7fa454b6a4268b89fe18043e8dd10f30a7b4c7ca
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35 #if $what.to_do == "get_data_and_produce_plot"
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36 &&
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37 #end if
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38
59c8bad5f6bc planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ commit 7fa454b6a4268b89fe18043e8dd10f30a7b4c7ca
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39 #if "produce_plot" in str($what.to_do)
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40 python3 '$__tool_directory__/kmd_hmdb_plot_generator.py' plot
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41
59c8bad5f6bc planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ commit 7fa454b6a4268b89fe18043e8dd10f30a7b4c7ca
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42 #if "get_data" in str($what.to_do)
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43 --input '$output_path'
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44 #else
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45 --input '$what.tsv_input'
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46 #end if
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47
59c8bad5f6bc planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ commit 7fa454b6a4268b89fe18043e8dd10f30a7b4c7ca
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48 #if $what.x_columns
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49 #for x in $what.x_columns
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50 --x-column '$x'
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51 #end for
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52 #end if
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53
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54 #if $what.y_columns
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55 #for y in $what.y_columns
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56 --y-column '$y'
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57 #end for
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58 #end if
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59
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60 #if $what.annotation_columns
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61 #for annotation_column in $what.annotation_columns
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62 --annotation-column '$annotation_column'
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63 #end for
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64 #end if
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65
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66 --output 'out.html'
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67
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68 && cat 'out.html' > '$output'
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69 #end if
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70 ]]>
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71 </command>
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72
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73 <inputs>
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74 <conditional name="what">
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75 <param name="to_do" type="select"
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76 label="What to do"
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77 >
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78 <option value="get_data">Only get data</option>
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79 <option value="produce_plot">Only produce plot</option>
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80 <option value="get_data_and_produce_plot" selected="true">
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81 Get data from database + Produce Plot
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82 </option>
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83 </param>
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84 <when value="produce_plot">
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85 <expand macro="produce_plot_inputs" />
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86 <expand macro="not_get_data" />
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87 </when>
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88 <when value="get_data">
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89 <expand macro="get_data_inputs" />
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90 <expand macro="not_produce_plot" />
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91 </when>
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92 <when value="get_data_and_produce_plot">
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93 <expand macro="get_data_inputs" />
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94 <expand macro="not_produce_plot" />
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95 </when>
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96 </conditional>
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97 </inputs>
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98
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99 <outputs>
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100 <expand macro="get_data_outputs" />
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101 <expand macro="produce_plot_outputs" />
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102 </outputs>
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103
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104 <tests>
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105 <test>
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106 <!-- #1 get_data with tolerance = 0.01 -->
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107 <param name="to_do" value="get_data" />
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108 <param name="mass_tolerance" value="0.01" />
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109 <param name="mz_ratio" value="303.05" />
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110 <param name="database" value="hmdb" />
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111 <param name="adducts" value="M+H" />
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112 <output name="output_path" file="get_data_tol_0.01.tsv" />
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113 </test>
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114 </tests>
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115
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116 <help><![CDATA[
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117
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118 This tool includes two utilities.
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119 One that retrieves data from the KMD HMDB API formated as a tsv file,
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120 and the other plots those data in a plotly graph.
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121
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122 The default behavior of the plot is to produce a plot of the kmd in
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123 in function of the nominal mass of the compound.
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124
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125 Compounds are retrieved using a query with default parameters:
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126 - mz default to @DEFAULT_MZ@
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127 - mz tolerance defaults to @DEFAULT_TOLERENCE@
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128 - adduct list defaults to "@DEFAULT_ADDUCT@"
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129 - database default to "@DEFAULT_DATABASE@", and possible values are one of:
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130
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131 - KMD Metabolites
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132 - HMDB
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133
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134 Those two utilities are usable independently, or sequentially in galaxy.
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135
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136 Multiple X / Y values in the X/Y column selection can be
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137 selected to produce a lot of graphs at once.
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138
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139 For example, imagine you have 5 columns in you tsv file,
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140 and those columns are named: A, B, C, D and F.
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141
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142 If you choose X = [A, C] and Y = [B],
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143 then you will get two graphs (in one single HTML file) with:
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144
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145 - f(A) = B
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146 - f(C) = B
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147
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148 But if you choose multiple values for both X and Y, you get
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149 all combinations of columns X and Y. For example, if you
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150 select X = [A, B] and Y = [C, D, E], then you will get six
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151 graphs on the same plot:
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152
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153 - f(A) = C
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154 - f(A) = D
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155 - f(A) = E
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156 - f(B) = C
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157 - f(B) = D
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158 - f(B) = E
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159
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160 All those graph's traces will be tooglable in the HTML page.
59c8bad5f6bc planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ commit 7fa454b6a4268b89fe18043e8dd10f30a7b4c7ca
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161 So don't hesitate to select a lot of parameters for X and Y!
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162
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163 ]]>
59c8bad5f6bc planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/kmd_hmdb_data_plot/ commit 7fa454b6a4268b89fe18043e8dd10f30a7b4c7ca
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164 </help>
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165 <citations></citations>
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166 <creator>
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167 <person
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168 honorificPrefix="Mx."
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169 givenName="Lain"
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170 familyName="Pavot"
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171 email="lain.pavot@inrae.fr"
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172 identifier="https://orcid.org/0009-0007-1841-4358"
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173 />
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174 </creator>
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175
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176 </tool>