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annotate build/tools/Sbml2Tab/Sbml2Tab.xml @ 10:6a112eaf8f38 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 71071300dd662ad01bd064abcf6866a192eeea95
author metexplore
date Mon, 03 Feb 2025 15:59:46 +0000
parents 0976a6257300
children 40c15b7467f1
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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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6a112eaf8f38 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 71071300dd662ad01bd064abcf6866a192eeea95
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2 <tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="2.0.0">
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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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6a112eaf8f38 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 71071300dd662ad01bd064abcf6866a192eeea95
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8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</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($r):
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0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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14 -rev "$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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37 <param name="in" value="toy_model.xml"/>
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38 <output ftype="tsv" name="out">
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39 <assert_contents>
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40 <has_n_lines n="8"/>
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41 <has_n_columns n="9"/>
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42 <has_text text="2.0 E[c] --&gt; D[c]"/>
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43 <has_text text="A[c] &lt;==&gt; B[c]"/>
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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="in" value="toy_model.xml"/>
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49 <param name="i" value="-&gt;"/>
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50 <param name="r" value="="/>
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51 <output ftype="tsv" name="out">
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52 <assert_contents>
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53 <has_n_lines n="8"/>
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54 <has_n_columns n="9"/>
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55 <has_text text="2.0 E[c] -&gt; D[c]"/>
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56 <has_text text="A[c] = B[c]"/>
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57 </assert_contents>
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58 </output>
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59 </test>
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60 </tests>
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61 <help><![CDATA[Create a tabulated file listing reaction attributes from a SBML file]]></help>
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62 <citations/>
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63 </tool>