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annotate tools/attributes/GetReactantsFromReactions/GetReactantsFromReactions.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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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="met4j_GetReactantsFromReactions" name="GetReactantsFromReactions" version="MET4J_VERSION_TEST">
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3 <description>Get reactants lists from a list of reactions and a GSMN.</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:MET4J_VERSION_TEST</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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41 <param name="sbml" value="XF_network.sbml"/>
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42 <param name="reactionFile" value="XF_network_R_Seed.tab"/>
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43 <output ftype="tsv" name="outputFile">
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44 <assert_contents>
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45 <has_text_matching expression="R_GLUN" n="4"/>
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46 <has_text_matching expression="R_ACGS" n="5"/>
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47 </assert_contents>
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48 </output>
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49 </test>
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50 <test>
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51 <param name="sbml" value="XF_network.sbml"/>
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52 <param name="reactionFile" value="XF_network_R_Seed.tab"/>
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53 <param name="printSubstrates" value="true"/>
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54 <output ftype="tsv" name="outputFile">
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55 <assert_contents>
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56 <has_text_matching expression="R_GLUN" n="2"/>
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57 <has_text_matching expression="R_ACGS" n="5"/>
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58 </assert_contents>
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59 </output>
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60 </test>
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61 <test>
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62 <param name="sbml" value="XF_network.sbml"/>
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63 <param name="reactionFile" value="XF_network_R_Seed.tab"/>
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64 <param name="printProducts" value="true"/>
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65 <output ftype="tsv" name="outputFile">
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66 <assert_contents>
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67 <has_text_matching expression="R_GLUN" n="2"/>
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68 <has_text_matching expression="R_ACGS" n="5"/>
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69 </assert_contents>
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70 </output>
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71 </test>
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72 </tests>
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73 <help><![CDATA[Get reactants lists from a list of reactions and a GSMN. 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 both substrates and products]]></help>
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74 <citations/>
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75 </tool>