Mercurial > repos > metexplore > met4j

annotate build/tools/ReactionDistanceMatrix/ReactionDistanceMatrix.xml @ 11:40c15b7467f1 draft default tip

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518
author metexplore
date Thu, 13 Feb 2025 15:08:22 +0000
parents 6a112eaf8f38
children
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <tool id="met4j_ReactionDistanceMatrix" name="ReactionDistanceMatrix" version="2.0.1">
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3 <description>Create a reaction to reaction distance matrix.</description>
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4 <xrefs>
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5 <xref type="bio.tools">met4j</xref>
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6 </xrefs>
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7 <requirements>
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8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ReactionDistanceMatrix -i "$inputPath"
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11 #if str($sideCompoundFile) != 'None':
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12 -sc "$sideCompoundFile"
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13 #end if
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14 $degree
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15 #if str($rExclude) != 'None':
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16 -re "$rExclude"
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17 #end if
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18 #if str($rxnFile) != 'None':
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19 -s "$rxnFile"
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20 #end if
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21 #if str($weightFile) != 'None':
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22 -w "$weightFile"
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23 #end if
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24 $undirected
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25 -o "$outputPath"
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26 ]]></command>
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27 <inputs>
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28 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
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29 <param argument="-sc" format="txt" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/>
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30 <param argument="-dw" checked="false" falsevalue="" label="penalize traversal of hubs by using degree square weighting (-w must not be set)" name="degree" truevalue="-dw" type="boolean" value="false"/>
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31 <param argument="-re" format="txt" label="an optional file containing list of reactions to ignore" name="rExclude" optional="true" type="data" value=""/>
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32 <param argument="-s" format="txt" label="an optional file containing list of reactions of interest." name="rxnFile" optional="true" type="data" value=""/>
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33 <param argument="-w" format="tsv" label="an optional file containing weights for compound pairs" name="weightFile" optional="true" type="data" value=""/>
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34 <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/>
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35 </inputs>
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36 <outputs>
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37 <data format="csv" name="outputPath"/>
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38 </outputs>
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39 <tests>
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40 <test>
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42 <param name="inputPath" value="toy_model.xml"/>
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44 <output ftype="csv" name="outputPath">
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46 <assert_contents>
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48 <has_n_lines n="8"/>
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50 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/>
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52 <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,Infinity,Infinity" n="1"/>
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54 <has_line_matching expression="reac2,Infinity,0.0,1.0,1.0,2.0,Infinity,Infinity" n="1"/>
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56 </assert_contents>
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58 </output>
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60 </test>
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61 <test>
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63 <param name="inputPath" value="toy_model.xml"/>
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65 <param name="undirected" value="true"/>
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67 <output ftype="csv" name="outputPath">
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69 <assert_contents>
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71 <has_n_lines n="8"/>
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73 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/>
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75 <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,5.0,4.0" n="1"/>
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77 <has_line_matching expression="reac2,1.0,0.0,1.0,1.0,2.0,4.0,3.0" n="1"/>
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79 </assert_contents>
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81 </output>
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83 </test>
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84 <test>
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86 <param name="inputPath" value="toy_model.xml"/>
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88 <param name="undirected" value="true"/>
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89
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90 <param name="sideCompoundFile" value="sides.txt"/>
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91
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92 <output ftype="csv" name="outputPath">
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93
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94 <assert_contents>
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95
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96 <has_n_lines n="8"/>
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97
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98 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/>
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99
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100 <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,5.0,4.0" n="1"/>
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101
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102 <has_line_matching expression="reac2,1.0,0.0,1.0,2.0,3.0,5.0,4.0" n="1"/>
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104 <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0,4.0,3.0" n="1"/>
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105
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106 <has_line_matching expression="reac4,2.0,2.0,1.0,0.0,1.0,3.0,2.0" n="1"/>
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107
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108 </assert_contents>
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109
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110 </output>
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111
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112 </test>
1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
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113 <test>
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115 <param name="inputPath" value="toy_model.xml"/>
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116
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117 <param name="undirected" value="true"/>
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118
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119 <param name="rExclude" value="rexclude.txt"/>
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120
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121 <output ftype="csv" name="outputPath">
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122
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123 <assert_contents>
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124
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125 <has_n_lines n="6"/>
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126
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127 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/>
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128
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129 <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/>
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131 <has_line_matching expression="reac2,1.0,0.0,1.0,1.0,2.0" n="1"/>
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133 <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0" n="1"/>
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134
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135 <has_line_matching expression="reac4,2.0,1.0,1.0,0.0,1.0" n="1"/>
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136
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137 <has_line_matching expression="reac5,3.0,2.0,2.0,1.0,0.0" n="1"/>
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138
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139 </assert_contents>
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140
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141 </output>
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142
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143 </test>
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144 <test>
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146 <param name="inputPath" value="toy_model.xml"/>
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148 <param name="undirected" value="true"/>
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149
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150 <param name="sideCompoundFile" value="sides.txt"/>
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151
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152 <param name="rExclude" value="rexclude.txt"/>
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154 <output ftype="csv" name="outputPath">
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156 <assert_contents>
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157
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158 <has_n_lines n="6"/>
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159
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160 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/>
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161
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162 <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/>
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164 <has_line_matching expression="reac2,1.0,0.0,1.0,2.0,3.0" n="1"/>
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166 <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0" n="1"/>
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167
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168 <has_line_matching expression="reac4,2.0,2.0,1.0,0.0,1.0" n="1"/>
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169
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170 <has_line_matching expression="reac5,3.0,3.0,2.0,1.0,0.0" n="1"/>
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172 </assert_contents>
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174 </output>
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176 </test>
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177 <test>
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178
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179 <param name="inputPath" value="toy_model.xml"/>
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180
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181 <param name="sideCompoundFile" value="sides.txt"/>
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182
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183 <param name="rExclude" value="rexclude.txt"/>
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184
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185 <output ftype="csv" name="outputPath">
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186
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187 <assert_contents>
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188
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189 <has_n_lines n="6"/>
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190
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191 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/>
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192
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193 <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/>
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194
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195 <has_line_matching expression="reac2,Infinity,0.0,1.0,2.0,3.0" n="1"/>
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196
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197 <has_line_matching expression="reac3,Infinity,Infinity,0.0,1.0,2.0" n="1"/>
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198
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199 <has_line_matching expression="reac4,Infinity,Infinity,Infinity,0.0,1.0" n="1"/>
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200
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201 <has_line_matching expression="reac5,Infinity,Infinity,Infinity,Infinity,0.0" n="1"/>
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203 </assert_contents>
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204
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205 </output>
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206
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207 </test>
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208 </tests>
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209 <help><![CDATA[Create a reaction to reaction distance matrix.
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210 The distance between two reactions is computed as the length of the shortest path connecting the two in the reaction graph, where two reactions are linked if they produce a metabolite consumed by the other or the other way around.
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211 An optional edge weighting can be used, turning the distances into the sum of edge weights in the lightest path, rather than the length of the shortest path.The default weighting use target's degree squared. Alternatively, custom weighting can be provided in a file. In that case, edges without weight are ignored during path search.
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212 If no edge weighting is set, it is recommended to provide a list of side compounds to ignore during network traversal.]]></help>
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213 <citations/>
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214 </tool>