Mercurial > repos > metexplore > met4j

annotate build/tools/SetNames/SetNames.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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <tool id="met4j_SetNames" name="SetNames" version="2.0.1">
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3 <description>Set names to network objects in a SBML file from a tabulated file containing the object ids and the names</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 attributes.SetNames#if str($colname) != 'nan':
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11 -cname "$colname"
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12 #end if
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13 #if str($colid):
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14 -ci "$colid"
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15 #end if
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16 $p
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17 $s
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18 #if str($o):
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19 -t "$o"
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20 #end if
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21 #if str($nSkip):
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22 -n "$nSkip"
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23 #end if
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24 -i "$sbml"
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25 #if str($tab) != 'None':
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26 -tab "$tab"
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27 #end if
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28 #if str($c):
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29 -c "$c"
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30 #end if
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31 -o "$out"
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32 ]]></command>
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33 <inputs>
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34 <param argument="-cname" label="[2] number of the column where are the names" name="colname" optional="true" type="integer" value="2"/>
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35 <param argument="-ci" label="[1] number of the column where are the object ids" name="colid" optional="true" type="text" value="1">
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36 <sanitizer invalid_char="_">
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37 <valid initial="string.printable"/>
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38 </sanitizer>
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39 </param>
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40 <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions and M_ to metabolites" name="p" truevalue="-p" type="boolean" value="false"/>
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41 <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/>
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42 <param argument="-t" label="[REACTION] Object type in the column id : REACTION;METABOLITE;GENE;PATHWAY" name="o" optional="true" type="text" value="REACTION">
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43 <sanitizer invalid_char="_">
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44 <valid initial="string.printable"/>
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45 </sanitizer>
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46 </param>
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47 <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0">
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48 <sanitizer invalid_char="_">
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49 <valid initial="string.printable"/>
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50 </sanitizer>
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51 </param>
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52 <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/>
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53 <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/>
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54 <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#">
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55 <sanitizer invalid_char="_">
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56 <valid initial="string.printable"/>
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57 </sanitizer>
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58 </param>
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59 </inputs>
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60 <outputs>
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61 <data format="sbml" name="out"/>
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62 </outputs>
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63 <tests>
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64 <test>
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65
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66 <param name="sbml" value="toy_model.xml"/>
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67
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68 <param name="tab" value="namesMetabolites.tsv"/>
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69
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70 <param name="o" value="METABOLITE"/>
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71
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72 <output ftype="sbml" name="out">
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73
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74 <assert_contents>
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75
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76 <is_valid_xml/>
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78 <has_line_matching expression=".*metaboliteA.*" n="1"/>
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79
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80 <has_line_matching expression=".*metaboliteB.*" n="1"/>
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81
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82 </assert_contents>
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83
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84 </output>
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85
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86 </test>
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87 <test>
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89 <param name="sbml" value="toy_model.xml"/>
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90
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91 <param name="tab" value="namesReactions.tsv"/>
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92
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93 <output ftype="sbml" name="out">
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94
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95 <assert_contents>
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40c15b7467f1 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518
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96
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97 <is_valid_xml/>
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40c15b7467f1 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518
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98
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99 <has_line_matching expression=".*reaction1.*" n="1"/>
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100
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101 <has_line_matching expression=".*reaction2.*" n="1"/>
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102
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103 </assert_contents>
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40c15b7467f1 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518
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104
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105 </output>
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106
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107 </test>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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108 <test>
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109
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110 <param name="sbml" value="XF_network.sbml"/>
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40c15b7467f1 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518
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111
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112 <param name="tab" value="namesPathways.tsv"/>
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40c15b7467f1 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518
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113
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114 <param name="o" value="PATHWAY"/>
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115
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116 <output ftype="sbml" name="out">
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40c15b7467f1 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518
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117
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118 <assert_contents>
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119
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120 <is_valid_xml/>
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121
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122 <has_line_matching expression=".*groups:name=.CEB.*" n="1"/>
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123
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124 <has_line_matching expression=".*groups:name=.NSP.*" n="1"/>
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125
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126 </assert_contents>
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127
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128 </output>
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129
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130 </test>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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131 <test>
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133 <param name="sbml" value="XF_network.sbml"/>
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134
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135 <param name="tab" value="namesGenes.tsv"/>
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136
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137 <param name="o" value="GENE"/>
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138
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139 <output ftype="sbml" name="out">
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140
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141 <assert_contents>
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142
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143 <is_valid_xml/>
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144
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145 <has_line_matching expression=".*fbc:name=.G1.*" n="1"/>
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146
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147 <has_line_matching expression=".*fbc:name=.G2.*" n="1"/>
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148
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149 </assert_contents>
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150
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151 </output>
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153 </test>
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154 </tests>
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155 <help><![CDATA[Set names to network objects in a SBML file from a tabulated file containing the object ids and the names
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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156 The ids must correspond between the tabulated file and the SBML file.
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157 If prefix or suffix is different in the SBML file, use the -p or the -s options.
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158 ]]></help>
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159 <citations/>
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160 </tool>