Mercurial > repos > metexplore > met4j

annotate tools/convert/SbmlWizard/SbmlWizard.xml @ 9:0976a6257300 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
author metexplore
date Fri, 31 Jan 2025 18:28:53 +0000
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0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <tool id="met4j_SbmlWizard" name="SbmlWizard" version="develop">
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3 <description>General SBML model processing</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:develop</container>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.SbmlWizard -i "$inputPath"
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11 #if str($inputSide) != 'None':
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12 -rc "$inputSide"
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13 #end if
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14 #if str($toKeepC) != 'None':
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15 -kc "$toKeepC"
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16 #end if
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17 $removeIsolated
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18 #if str($inputReactions) != 'None':
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19 -rr "$inputReactions"
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20 #end if
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21 #if str($toKeepR) != 'None':
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22 -kr "$toKeepR"
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23 #end if
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24 $removeNoFlux
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25 #if str($mergingStrat):
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26 -mc "$mergingStrat"
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27 #end if
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28 $removeDuplicated
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29 #if str($exchangeCompToRemove):
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30 -rEX "$exchangeCompToRemove"
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31 #end if
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32 -o "$outputPath"
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33 ]]></command>
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34 <inputs>
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35 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
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36 <param argument="-rc" format="txt" label="file containing identifiers of compounds to remove from the metabolic network" name="inputSide" optional="true" type="data" value=""/>
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37 <param argument="-kc" format="txt" label="file containing identifiers of compounds to keep from the metabolic network" name="toKeepC" optional="true" type="data" value=""/>
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38 <param argument="-ric" checked="false" falsevalue="" label="remove isolated compounds (not involved in any reaction)" name="removeIsolated" truevalue="-ric" type="boolean" value="false"/>
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39 <param argument="-rr" format="txt" label="file containing identifiers of reactions to remove from the metabolic network" name="inputReactions" optional="true" type="data" value=""/>
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40 <param argument="-kr" format="txt" label="file containing identifiers of reactions to keep from the metabolic network" name="toKeepR" optional="true" type="data" value=""/>
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41 <param argument="-r0" checked="false" falsevalue="" label="remove reactions with lower and upper flux bounds both set to 0.0" name="removeNoFlux" truevalue="-r0" type="boolean" value="false"/>
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42 <param argument="-mc" label="merge compartments using the provided strategy. No merge by default. &quot;by_name&quot; can be used if names are consistent and unambiguous across compartments, &quot;by_id&quot; can be used if compartment suffix is present in compounds identifiers (id in form &quot;xxx_y&quot; with xxx as base identifier and y as compartment label)." name="mergingStrat" optional="true" type="select" value="no">
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43 <option selected="true" value="no">no</option>
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44 <option value="by_name">by_name</option>
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45 <option value="by_id">by_id</option>
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46 </param>
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47 <param argument="-rdr" checked="false" falsevalue="" label="remove duplicated reactions (same reactants, same GPR)" name="removeDuplicated" truevalue="-rdr" type="boolean" value="false"/>
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48 <param argument="-rEX" label="remove exchange reactions and species from given exchange compartment identifier" name="exchangeCompToRemove" optional="true" type="text" value="">
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49 <sanitizer invalid_char="_">
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50 <valid initial="string.printable"/>
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51 </sanitizer>
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52 </param>
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53 </inputs>
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54 <outputs>
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55 <data format="sbml" name="outputPath"/>
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56 </outputs>
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57 <tests>
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58 <test>
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65 <param name="inputPath" value="Human-GEM_pathways.xml"/>
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72 <param name="removeIsolated" value="true"/>
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79 <param name="removeNoFlux" value="true"/>
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86 <param name="mergingStrat" value="by_id"/>
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93 <param name="removeDuplicated" value="true"/>
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97
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98
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99
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metexplore
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100 <param name="exchangeCompToRemove" value="s"/>
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101
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102
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103
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104
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105
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106
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metexplore
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107 <output ftype="sbml" name="outputPath">
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108
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109
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110
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111
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112
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113
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metexplore
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114 <assert_contents>
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115
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116
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117
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118
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119
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120
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metexplore
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121 <has_text text="&lt;/sbml&gt;"/>
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122
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123
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124
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125
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126
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127
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128 </assert_contents>
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129
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130
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131
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132
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133
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134
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135 </output>
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137
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138
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140
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141
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142 </test>
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metexplore
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143 <test>
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144
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145
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146
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148
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149
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metexplore
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150 <param name="inputPath" value="XF_network.sbml"/>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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151
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152
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155
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156
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157 <param name="removeIsolated" value="true"/>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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158
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159
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160
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161
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162
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163
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164 <param name="removeNoFlux" value="true"/>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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165
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166
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167
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168
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169
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170
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171 <param name="removeDuplicated" value="true"/>
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172
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174
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175
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176
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178 <param name="inputSide" value="XF_network_C_Side.tab"/>
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179
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181
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183
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184
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185 <param name="inputReactions" value="XF_network_R_Seed.tab"/>
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186
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0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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192 <output ftype="sbml" name="outputPath">
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193
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194
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196
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197
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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199 <assert_contents>
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0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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206 <has_text text="&lt;/sbml&gt;"/>
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213 </assert_contents>
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220 </output>
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227 </test>
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228 </tests>
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229 <help><![CDATA[General SBML model processing including compound removal (such as side compounds or isolated compounds), reaction removal (ex. blocked or exchange reaction), and compartment merging]]></help>
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230 <citations/>
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231 </tool>