Mercurial > repos > metexplore > met4j

annotate tools/convert/Sbml2Tab/Sbml2Tab.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
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="2.0.1">
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3 <description>Create a tabulated file listing reaction attributes from 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: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 convert.Sbml2Tab#if str($i):
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11 -irr "$i"
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12 #end if
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13 #if str($r):
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14 -rev "$r"
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15 #end if
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16 -i "$in"
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17 -o "$out"
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18 ]]></command>
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19 <inputs>
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20 <param argument="-irr" label="[--&gt;] String for irreversible reaction" name="i" optional="true" type="text" value="--&gt;">
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21 <sanitizer invalid_char="_">
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22 <valid initial="string.printable"/>
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23 </sanitizer>
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24 </param>
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25 <param argument="-rev" label="[&lt;==&gt;] String for reversible reaction" name="r" optional="true" type="text" value="&lt;==&gt;">
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26 <sanitizer invalid_char="_">
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27 <valid initial="string.printable"/>
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28 </sanitizer>
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29 </param>
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30 <param argument="-i" format="sbml" label="Sbml file" name="in" optional="false" type="data" value=""/>
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31 </inputs>
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32 <outputs>
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33 <data format="tsv" name="out"/>
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34 </outputs>
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35 <tests>
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36 <test>
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38 <param name="in" value="toy_model.xml"/>
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40 <output ftype="tsv" name="out">
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42 <assert_contents>
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44 <has_n_lines n="8"/>
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46 <has_n_columns n="9"/>
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48 <has_text text="2.0 E[c] --&gt; D[c]"/>
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50 <has_text text="A[c] &lt;==&gt; B[c]"/>
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52 </assert_contents>
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54 </output>
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56 </test>
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57 <test>
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59 <param name="in" value="toy_model.xml"/>
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61 <param name="i" value="-&gt;"/>
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63 <param name="r" value="="/>
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65 <output ftype="tsv" name="out">
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67 <assert_contents>
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69 <has_n_lines n="8"/>
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71 <has_n_columns n="9"/>
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73 <has_text text="2.0 E[c] -&gt; D[c]"/>
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75 <has_text text="A[c] = B[c]"/>
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77 </assert_contents>
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79 </output>
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81 </test>
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82 </tests>
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83 <help><![CDATA[Create a tabulated file listing reaction attributes from a SBML file]]></help>
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84 <citations/>
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85 </tool>