Mercurial > repos > recetox > ipapy2_compute_bio

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
author recetox
date Fri, 16 May 2025 08:02:29 +0000
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ca72f5330bc9 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
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1 <tool id="ipapy2_compute_bio" name="ipaPy2 compute bio" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
ca72f5330bc9 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
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2 <description>compute list of biochemical connections to improve annotation accuracy</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
ca72f5330bc9 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
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7 <expand macro="requirements"/>
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8
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9 <command detect_errors="exit_code"><![CDATA[
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10 python3 '${__tool_directory__}/ipapy2_compute_bio.py'
ca72f5330bc9 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
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11 --input_dataset_database '${MS1_DB}' '${MS1_DB.ext}'
ca72f5330bc9 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
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12 --input_dataset_annotations '${annotations}' '${annotations.ext}'
ca72f5330bc9 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
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13 --biochemical_mode '${biochemical_mode.biochemical_mode}'
ca72f5330bc9 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
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14 #if $biochemical_mode.biochemical_mode == "connections"
ca72f5330bc9 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ipapy2 commit 64b61ff2823b4f54868c0ab7a4c0dc49eaf2979a
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15 --connection_list '${biochemical_mode.connection_list}'
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16 #end if
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17 --output_dataset "${compute_bio_output}" "${compute_bio_output.ext}"
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18 --ncores \${GALAXY_SLOTS:-1}
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19 ]]></command>
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21 <inputs>
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22 <param label="MS1 DB table" name="MS1_DB" type="data" format="csv,tsv,tabular,parquet" help="pandas dataframe containing the MS1 database."/>
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23 <param label="annotations" name="annotations" type="data" format="csv,tsv,tabular,parquet" optional="true" help="pandas dataframe containing all the possible annotations for the measured features."/>
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24 <conditional name="biochemical_mode">
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25 <param name="biochemical_mode" type="select" label="biochemical mode"
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26 help="connections are computed based on the reactions or connections.">
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27 <option value="reactions" selected="true">reactions</option>
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28 <option value="connections">connections</option>
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29 </param>
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30 <when value="reactions">
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31 </when>
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32 <when value="connections">
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33 <param name="connection_list" type="select" multiple="true" label="connections list provided" help="list of possible connections between compounds defined as formulas.">
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34 <option value="C3H5NO">C3H5NO</option>
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35 <option value="C6H12N4O">C6H12N4O</option>
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36 <option value="C6H10N2O3S2">C6H10N2O3S2</option>
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37 <option value="C3H5NOS">C3H5NOS</option>
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38 <option value="C5H7NO3">C5H7NO3</option>
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39 <option value="C5H8N2O2">C5H8N2O2</option>
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40 <option value="C2H3NO">C2H3NO</option>
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41 <option value="C6H7N3O">C6H7N3O</option>
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42 <option value="C6H11NO">C6H11NO</option>
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43 <option value="C6H12N2O">C6H12N2O</option>
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44 <option value="C5H9NOS">C5H9NOS</option>
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45 <option value="C9H9NO">C9H9NO</option>
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46 <option value="C5H7NO">C5H7NO</option>
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47 <option value="C3H5NO2">C3H5NO2</option>
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48 <option value="C4H7NO2">C4H7NO2</option>
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49 <option value="C11H10N2O">C11H10N2O</option>
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50 <option value="C9H9NO2">C9H9NO2</option>
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51 <option value="C5H9NO">C5H9NO</option>
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52 <option value="C4H4O2">C4H4O2</option>
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53 <option value="C3H5O">C3H5O</option>
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54 <option value="C10H12N5O6P">C10H12N5O6P</option>
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55 <option value="C10H15N2O3S">C10H15N2O3S</option>
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56 <option value="C10H14N2O2S">C10H14N2O2S</option>
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57 <option value="CH2ON">CH2ON</option>
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58 <option value="C21H34N7O16P3S">C21H34N7O16P3S</option>
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59 <option value="C21H33N7O15P3S">C21H33N7O15P3S</option>
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60 <option value="C10H15N3O5S">C10H15N3O5S</option>
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61 <option value="C5H7">C5H7</option>
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62 <option value="C3H2O3">C3H2O3</option>
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63 <option value="C16H30O">C16H30O</option>
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64 <option value="C8H8NO5P">C8H8NO5P</option>
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65 <option value="CH3N2O">CH3N2O</option>
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66 <option value="C5H4N5">C5H4N5</option>
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67 <option value="C10H11N5O3">C10H11N5O3</option>
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68 <option value="C10H13N5O9P2">C10H13N5O9P2</option>
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69 <option value="C9H13N3O10P2">C9H13N3O10P2</option>
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70 <option value="C9H12N3O7P">C9H12N3O7P</option>
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71 <option value="C4H4N3O">C4H4N3O</option>
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72 <option value="C10H13N5O10P2">C10H13N5O10P2</option>
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73 <option value="C10H12N5O7P">C10H12N5O7P</option>
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74 <option value="C5H4N5O">C5H4N5O</option>
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75 <option value="C10H11N5O4">C10H11N5O4</option>
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76 <option value="C10H14N2O10P2">C10H14N2O10P2</option>
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77 <option value="C10H12N2O4">C10H12N2O4</option>
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78 <option value="C5H5N2O2">C5H5N2O2</option>
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79 <option value="C10H13N2O7P">C10H13N2O7P</option>
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80 <option value="C9H12N2O11P2">C9H12N2O11P2</option>
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81 <option value="C9H11N2O8P">C9H11N2O8P</option>
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82 <option value="C4H3N2O2">C4H3N2O2</option>
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83 <option value="C9H10N2O5">C9H10N2O5</option>
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84 <option value="C2H3O2">C2H3O2</option>
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85 <option value="C2H2O">C2H2O</option>
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86 <option value="C2H2">C2H2</option>
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87 <option value="CO2">CO2</option>
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88 <option value="CHO2">CHO2</option>
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89 <option value="H2O">H2O</option>
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90 <option value="H3O6P2">H3O6P2</option>
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91 <option value="C2H4">C2H4</option>
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92 <option value="CO">CO</option>
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93 <option value="C2O2">C2O2</option>
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94 <option value="H2">H2</option>
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95 <option value="O">O</option>
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96 <option value="P">P</option>
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97 <option value="CH2">CH2</option>
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98 <option value="HPO3">HPO3</option>
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99 <option value="NH2">NH2</option>
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100 <option value="PP">PP</option>
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101 <option value="NH">NH</option>
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102 <option value="SO3">SO3</option>
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103 <option value="N">N</option>
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104 <option value="C6H10O5">C6H10O5</option>
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105 <option value="C6H10O6">C6H10O6</option>
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106 <option value="C5H8O4">C5H8O4</option>
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107 <option value="C12H20O11">C12H20O11</option>
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108 <option value="C6H11O8P">C6H11O8P</option>
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109 <option value="C6H8O6">C6H8O6</option>
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110 <option value="C4H6N2O2">C4H6N2O2</option>
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111 <option value="C4H5NO3">C4H5NO3</option>
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112 <option value="C18H30O15">C18H30O15</option>
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113 </param>
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114 </when>
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115 </conditional>
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116 </inputs>
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117
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118 <outputs>
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119 <data label="${tool.name} on ${on_string}" name="compute_bio_output" format_source="MS1_DB"/>
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120 </outputs>
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121
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122 <tests>
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123 <test>
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124 <param name="MS1_DB" value="compute_bio_db.csv"/>
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125 <param name="annotations" value="clean_annotations.csv"/>
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126 <param name="biochemical_mode" value="reactions"/>
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127 <!-- Not the best way to test, but the results are stochastic hence difficult to test-->
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128 <output name="compute_bio_output">
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129 <assert_contents>
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130 <has_text text="C00079" />
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131 <has_n_columns n="2" sep=","/>
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132 <has_n_lines n="2" delta="3" />
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133 </assert_contents>
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134 </output>
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135 </test>
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136 </tests>
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137
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138 <help><![CDATA[
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139
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140 .. _ipapy2_compute_bio:
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141
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142 ===============================
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143 ipaPy2 Compute Bio Connections
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144 ===============================
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145
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146 **Tool Description**
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147
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148 This tool generates a table of biochemical connections between compounds in your MS1 database. These connections are used by the IPA method to update annotation probabilities by considering known biochemical relationships, such as reactions or user-defined connections. The resulting table can be used in downstream annotation refinement tools (e.g., the ipaPy2 Gibbs sampler).
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149
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150 How it works
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151 ------------
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152
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153 - The tool examines the compounds in your MS1 database and determines which pairs are biochemically related.
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154 - Two modes are available:
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155
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156 - **Reactions mode**: Connections are computed based on known biochemical reactions (recommended for most users).
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157 - **Connections mode**: Connections are computed based on a user-provided list of possible connections (e.g., specific transformation formulas).
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158
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159 - The output is a two-column table listing all pairs of compounds that are considered biochemically connected.
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160
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161 Inputs
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162 ------
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163
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164 1. **MS1 DB table**
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165 A table (CSV, TSV, Parquet, or Tabular) containing the MS1 database of compounds.
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166
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167 2. **Annotations**
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168 (Optional) Table of possible annotations for the measured features.
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169
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170 3. **Biochemical mode**
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171 - **reactions**: Compute connections based on known biochemical reactions.
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172 - **connections**: Use a user-provided list of possible connections (formulas).
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173
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174 4. **Connections list**
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175 (Only required if using "connections" mode)
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176 A list of possible connections between compounds, defined as formulas.
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177
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178 Outputs
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179 -------
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180
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181 - **compute_bio_output**
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182 A two-column table listing all pairs of compounds that are considered biochemically connected. This table can be used as input for downstream annotation refinement tools.
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183
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184 Example
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185 -------
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186
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187 Suppose you have an MS1 database (`compute_bio_db.csv`) and want to compute biochemical connections using the reactions mode:
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188
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189 .. code-block::
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190
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191 MS1_DB: compute_bio_db.csv
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192 biochemical_mode: reactions
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193
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194 Alternatively, to use a custom list of connections:
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195
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196 .. code-block::
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197
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198 MS1_DB: compute_bio_db.csv
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199 biochemical_mode: connections
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200 connection_list: [C2H4O2, C6H12O6, ...]
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201
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202 Notes
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203 -----
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204
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205 - The output table is essential for integrating biochemical knowledge into annotation refinement.
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206 - Ensure your input files are correctly formatted and contain the required columns.
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207 - The tool supports multiple file formats for flexibility.
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208
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209 References
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210 ----------
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211
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212 - For more details on biochemical connection computation and its use in IPA, refer to the ipaPy2 documentation or associated publications.
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213
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214 ]]></help>
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215
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216 <expand macro="citations"/>
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217 </tool>