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annotate build/tools/ReactionDistanceMatrix/ReactionDistanceMatrix.xml @ 8:1274e2a62479 draft default tip

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
author metexplore
date Wed, 26 Jul 2023 15:33:45 +0000
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8
1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
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1 <?xml version="1.0" encoding="UTF-8"?>
1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
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2 <tool id="met4j_ReactionDistanceMatrix" name="ReactionDistanceMatrix" version="1.5.0">
1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
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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:1.5.0</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 "$inputPath"
1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
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11 #if str($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=""/>
1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
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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"/>
1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
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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=""/>
1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
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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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41 <param name="inputPath" value="toy_model.xml"/>
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42 <output ftype="csv" name="outputPath">
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43 <assert_contents>
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44 <has_n_lines n="8"/>
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45 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/>
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46 <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,Infinity,Infinity" n="1"/>
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47 <has_line_matching expression="reac2,Infinity,0.0,1.0,1.0,2.0,Infinity,Infinity" n="1"/>
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48 </assert_contents>
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49 </output>
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50 </test>
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51 <test>
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52 <param name="inputPath" value="toy_model.xml"/>
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53 <param name="undirected" value="true"/>
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54 <output ftype="csv" name="outputPath">
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55 <assert_contents>
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56 <has_n_lines n="8"/>
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57 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/>
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58 <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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59 <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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60 </assert_contents>
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61 </output>
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62 </test>
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63 <test>
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64 <param name="inputPath" value="toy_model.xml"/>
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65 <param name="undirected" value="true"/>
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66 <param name="sideCompoundFile" value="sides.txt"/>
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67 <output ftype="csv" name="outputPath">
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68 <assert_contents>
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69 <has_n_lines n="8"/>
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70 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/>
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71 <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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72 <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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73 <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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74 <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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75 </assert_contents>
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76 </output>
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77 </test>
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78 <test>
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79 <param name="inputPath" value="toy_model.xml"/>
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80 <param name="undirected" value="true"/>
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81 <param name="rExclude" value="rexclude.txt"/>
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82 <output ftype="csv" name="outputPath">
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83 <assert_contents>
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84 <has_n_lines n="6"/>
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85 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/>
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86 <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/>
1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
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87 <has_line_matching expression="reac2,1.0,0.0,1.0,1.0,2.0" n="1"/>
1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
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88 <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0" n="1"/>
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89 <has_line_matching expression="reac4,2.0,1.0,1.0,0.0,1.0" n="1"/>
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90 <has_line_matching expression="reac5,3.0,2.0,2.0,1.0,0.0" n="1"/>
1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
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91 </assert_contents>
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92 </output>
1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
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93 </test>
1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
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94 <test>
1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
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95 <param name="inputPath" value="toy_model.xml"/>
1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
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96 <param name="undirected" value="true"/>
1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
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97 <param name="sideCompoundFile" value="sides.txt"/>
1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
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98 <param name="rExclude" value="rexclude.txt"/>
1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
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99 <output ftype="csv" name="outputPath">
1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
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100 <assert_contents>
1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
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101 <has_n_lines n="6"/>
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102 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/>
1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
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103 <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/>
1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
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104 <has_line_matching expression="reac2,1.0,0.0,1.0,2.0,3.0" n="1"/>
1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
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105 <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0" n="1"/>
1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
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106 <has_line_matching expression="reac4,2.0,2.0,1.0,0.0,1.0" n="1"/>
1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
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107 <has_line_matching expression="reac5,3.0,3.0,2.0,1.0,0.0" n="1"/>
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108 </assert_contents>
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109 </output>
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110 </test>
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111 <test>
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112 <param name="inputPath" value="toy_model.xml"/>
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113 <param name="sideCompoundFile" value="sides.txt"/>
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114 <param name="rExclude" value="rexclude.txt"/>
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115 <output ftype="csv" name="outputPath">
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116 <assert_contents>
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117 <has_n_lines n="6"/>
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118 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/>
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119 <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/>
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120 <has_line_matching expression="reac2,Infinity,0.0,1.0,2.0,3.0" n="1"/>
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121 <has_line_matching expression="reac3,Infinity,Infinity,0.0,1.0,2.0" n="1"/>
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122 <has_line_matching expression="reac4,Infinity,Infinity,Infinity,0.0,1.0" n="1"/>
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123 <has_line_matching expression="reac5,Infinity,Infinity,Infinity,Infinity,0.0" n="1"/>
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124 </assert_contents>
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125 </output>
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126 </test>
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127 </tests>
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128 <help><![CDATA[Create a reaction to reaction distance matrix.
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129 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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130 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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131 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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132 <citations/>
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133 </tool>