Mercurial > repos > metexplore > met4j

annotate tools/attributes/GetReactantsFromReactions/GetReactantsFromReactions.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
parents 7a6f2380fc1d
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <tool id="met4j_GetReactantsFromReactions" name="GetReactantsFromReactions" version="develop">
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3 <description>Get reactant lists from a list of reactions and a SBML file.</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 attributes.GetReactantsFromReactions -i "$sbml"
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11 -r "$reactionFile"
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12 #if str($sep):
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13 -sep "$sep"
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14 #end if
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15 $hasHeader
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16 #if str($i) != 'nan':
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17 -col "$i"
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18 #end if
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19 $printSubstrates
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20 $printProducts
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21 -o "$outputFile"
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22 ]]></command>
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23 <inputs>
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24 <param argument="-i" format="sbml" label="Input SBML file" name="sbml" optional="false" type="data" value=""/>
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25 <param argument="-r" format="tsv" label="Input Reaction file" name="reactionFile" optional="false" type="data" value=""/>
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26 <param argument="-sep" label="Separator in reaction file" name="sep" optional="true" type="text" value="&#9;">
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27 <sanitizer invalid_char="_">
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28 <valid initial="string.printable"/>
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29 </sanitizer>
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30 </param>
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31 <param argument="-header" checked="false" falsevalue="" label="Skip reaction file header" name="hasHeader" truevalue="-header" type="boolean" value="false"/>
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32 <param argument="-col" label="Column number in reaction file (first as 1)" name="i" optional="true" type="integer" value="1"/>
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33 <param argument="-s" checked="false" falsevalue="" label="Extract substrates only" name="printSubstrates" truevalue="-s" type="boolean" value="false"/>
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34 <param argument="-p" checked="false" falsevalue="" label="Extract products only" name="printProducts" truevalue="-p" type="boolean" value="false"/>
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35 </inputs>
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36 <outputs>
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37 <data format="tsv" name="outputFile"/>
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38 </outputs>
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39 <tests>
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40 <test>
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52 <param name="sbml" value="XF_network.sbml"/>
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64 <param name="reactionFile" value="XF_network_R_Seed.tab"/>
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76 <output ftype="tsv" name="outputFile">
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88 <assert_contents>
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99
3
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
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100 <has_text_matching expression="R_GLUN" n="4"/>
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111
3
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
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112 <has_text_matching expression="R_ACGS" n="5"/>
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123
3
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
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124 </assert_contents>
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135
3
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
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136 </output>
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147
3
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
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148 </test>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
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149 <test>
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160
3
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
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161 <param name="sbml" value="XF_network.sbml"/>
9
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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173 <param name="reactionFile" value="XF_network_R_Seed.tab"/>
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184
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185 <param name="printSubstrates" value="true"/>
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0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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196
3
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197 <output ftype="tsv" name="outputFile">
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3
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209 <assert_contents>
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221 <has_text_matching expression="R_GLUN" n="2"/>
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233 <has_text_matching expression="R_ACGS" n="5"/>
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244
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245 </assert_contents>
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256
3
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
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257 </output>
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268
3
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
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269 </test>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
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270 <test>
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3
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metexplore
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282 <param name="sbml" value="XF_network.sbml"/>
9
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294 <param name="reactionFile" value="XF_network_R_Seed.tab"/>
9
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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305
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306 <param name="printProducts" value="true"/>
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318 <output ftype="tsv" name="outputFile">
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329
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330 <assert_contents>
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341
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342 <has_text_matching expression="R_GLUN" n="2"/>
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353
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6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
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354 <has_text_matching expression="R_ACGS" n="5"/>
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365
3
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
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366 </assert_contents>
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377
3
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378 </output>
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389
3
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
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390 </test>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
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391 </tests>
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392 <help><![CDATA[Get reactant lists from a list of reactions and a Sbml file. Output a tab-separated file with one row per reactant, reaction identifiers in first column, reactant identifiers in second column. It can provides substrates, products, or both (by default). In the case of reversible reactions, all reactants are considered as both substrates and products]]></help>
3
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
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393 <citations/>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
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394 </tool>