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annotate tools/attributes/ExtractPathways/ExtractPathways.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
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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_ExtractPathways" name="ExtractPathways" version="2.0.1">
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3 <description>Extract pathway(s) from a SBML file and create a sub-network 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: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.ExtractPathways -i "$inputPath"
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11 -p "$pathwayId"
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12 -o "$outputPath"
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13 ]]></command>
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14 <inputs>
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15 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
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16 <param argument="-p" label="pathway identifiers, separated by &quot;+&quot; sign if more than one" name="pathwayId" optional="false" type="text" value="">
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17 <sanitizer invalid_char="_">
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18 <valid initial="string.printable"/>
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19 </sanitizer>
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20 </param>
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21 </inputs>
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22 <outputs>
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23 <data format="sbml" name="outputPath"/>
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24 </outputs>
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25 <tests>
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26 <test>
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28 <param name="inputPath" value="XF_network.sbml"/>
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30 <param name="pathwayId" value="Citric_Acid_Cycle+Folate_Metabolism+toto"/>
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32 <output ftype="sbml" name="outputPath">
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34 <assert_contents>
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36 <is_valid_xml/>
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38 <has_line_matching expression=".*&lt;reaction.*" n="17"/>
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40 <has_line_matching expression=".*groups:id=.*" n="2"/>
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42 </assert_contents>
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44 </output>
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46 </test>
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47 </tests>
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48 <help><![CDATA[Extract pathway(s) from a SBML file and create a sub-network SBML file]]></help>
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49 <citations/>
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50 </tool>