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comparison tools/convert/Tab2Sbml/Tab2Sbml.xml @ 2:e69a78624877 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit cb957f5d5540a48293fe8487c0cfad78ab439d7c
author metexplore
date Tue, 19 Jul 2022 14:20:07 +0000
parents 9b162ee6ff8e
children 6bd9aad9626d
comparison
equal deleted inserted replaced
1:9b162ee6ff8e 2:e69a78624877
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="0.12.0"> 2 <tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="1.0.1">
3 <description>Create a Sbml File from a tabulated file that contains the reaction ids and the formulas</description> 3 <description>Create a Sbml File from a tabulated file that contains the reaction ids and the formulas</description>
4 <xrefs> 4 <xrefs>
5 <xref type="bio.tools">met4j</xref> 5 <xref type="bio.tools">met4j</xref>
6 </xrefs> 6 </xrefs>
7 <requirements> 7 <requirements>
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Tab2Sbml#if str($colid) != 'nan': 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Tab2Sbml#if str($colid) != 'nan':
11 -ci "$colid" 11 -ci "$colid"
12 #end if 12 #end if
13 #if str($colformula) != 'nan': 13 #if str($colformula) != 'nan':
22 -i "$i" 22 -i "$i"
23 #end if 23 #end if
24 #if str($r): 24 #if str($r):
25 -r "$r" 25 -r "$r"
26 #end if 26 #end if
27 #if str($in) != 'None':
28 -in "$in" 27 -in "$in"
29 #end if
30 #if str($id): 28 #if str($id):
31 -id "$id" 29 -id "$id"
32 #end if 30 #end if
33 $createCompartment 31 $createCompartment
34 #if str($defaultCompartment): 32 #if str($defaultCompartment):
57 <param argument="-r" label="[&lt;==&gt;] String for reversible reaction" name="r" optional="true" type="text" value="&lt;==&gt;"> 55 <param argument="-r" label="[&lt;==&gt;] String for reversible reaction" name="r" optional="true" type="text" value="&lt;==&gt;">
58 <sanitizer invalid_char="_"> 56 <sanitizer invalid_char="_">
59 <valid initial="string.printable"/> 57 <valid initial="string.printable"/>
60 </sanitizer> 58 </sanitizer>
61 </param> 59 </param>
62 <param argument="-in" format="tsv" label="Tabulated file" name="in" optional="true" type="data" value=""/> 60 <param argument="-in" format="tsv" label="Tabulated file" name="in" optional="false" type="data" value=""/>
63 <param argument="-id" label="[NA] Model id written in the SBML file" name="id" optional="true" type="text" value="NA"> 61 <param argument="-id" label="[NA] Model id written in the SBML file" name="id" optional="true" type="text" value="NA">
64 <sanitizer invalid_char="_"> 62 <sanitizer invalid_char="_">
65 <valid initial="string.printable"/> 63 <valid initial="string.printable"/>
66 </sanitizer> 64 </sanitizer>
67 </param> 65 </param>