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annotate tools/attributes/ExtractSbmlAnnot/ExtractSbmlAnnot.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
parents 7a6f2380fc1d
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dcd16521b969 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="met4j_ExtractSbmlAnnot" name="ExtractSbmlAnnot" version="MET4J_VERSION_TEST">
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3 <description>Extract databases' references from SBML annotations or notes.</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.ExtractSbmlAnnot -i "$inputPath"
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11 -export "$export"
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12 -db "$db"
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13 $uniq
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14 $skip
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15 -o "$outputPath"
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16 ]]></command>
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17 <inputs>
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18 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
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19 <param argument="-export" label="the type of entity to extract annotation, either metabolite, reaction, or gene" name="export" optional="false" type="select" value="METABOLITE">
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20 <option selected="true" value="METABOLITE">METABOLITE</option>
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21 <option value="REACTION">REACTION</option>
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22 <option value="GENE">GENE</option>
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23 </param>
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24 <param argument="-db" label="name of the referenced database to export annotations from, as listed in notes or identifiers.org base uri" name="db" optional="false" type="text" value="">
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25 <sanitizer invalid_char="_">
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26 <valid initial="string.printable"/>
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27 </sanitizer>
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28 </param>
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29 <param argument="-uniq" checked="false" falsevalue="" label="keep only one identifier if multiple are referenced for the same entity" name="uniq" truevalue="-uniq" type="boolean" value="false"/>
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30 <param argument="-skip" checked="false" falsevalue="" label="Skip entities without the selected annotations, by default output them with NA value" name="skip" truevalue="-skip" type="boolean" value="false"/>
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31 </inputs>
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32 <outputs>
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33 <data format="tsv" name="outputPath"/>
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="inputPath" value="Human-GEM_pathways.xml"/>
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38 <param name="export" value="METABOLITE"/>
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39 <param name="db" value="metanetx.chemical"/>
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40 <output ftype="tsv" name="outputPath">
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41 <assert_contents>
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42 <has_n_lines n="146"/>
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43 <has_n_columns n="2"/>
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44 </assert_contents>
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45 </output>
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46 </test>
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47 <test>
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48 <param name="inputPath" value="Human-GEM_pathways.xml"/>
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49 <param name="export" value="METABOLITE"/>
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50 <param name="db" value="metanetx.chemical"/>
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51 <param name="skip" value="true"/>
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52 <output ftype="tsv" name="outputPath">
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53 <assert_contents>
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54 <has_n_lines n="145"/>
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55 <has_n_columns n="2"/>
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56 </assert_contents>
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57 </output>
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58 </test>
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59 <test>
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60 <param name="inputPath" value="Human-GEM_pathways.xml"/>
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61 <param name="export" value="METABOLITE"/>
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62 <param name="db" value="metanetx.chemical"/>
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63 <param name="skip" value="true"/>
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64 <param name="uniq" value="true"/>
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65 <output ftype="tsv" name="outputPath">
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66 <assert_contents>
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67 <has_n_lines n="111"/>
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68 <has_n_columns n="2"/>
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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[Extract databases' references from SBML annotations or notes. The references are exported as a tabulated file with one column with the SBML compound, reaction or gene identifiers, and one column with the corresponding database identifier.The name of the targeted database need to be provided under the same form than the one used in the notes field or the identifiers.org uri]]></help>
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74 <citations/>
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75 </tool>