comparison build/tools/ScopeNetwork/ScopeNetwork.xml @ 6:7a6f2380fc1d draft

planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
author metexplore
date Wed, 17 May 2023 13:26:37 +0000
parents
children 1436e9cde9c9
comparison
equal deleted inserted replaced
5:35c9abcd8934 6:7a6f2380fc1d
1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="1.3.0">
3 <description>Perform a network expansion from a set of compound seeds to create a scope network</description>
4 <xrefs>
5 <xref type="bio.tools">met4j</xref>
6 </xrefs>
7 <requirements>
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ScopeNetwork -i "$sbmlFilePath"
11 -s "$seedsFilePath"
12 #if str($sideCompoundFile) != 'None':
13 -sc "$sideCompoundFile"
14 #end if
15 $includeSides
16 #if str($reactionToIgnoreFile) != 'None':
17 -ir "$reactionToIgnoreFile"
18 #end if
19 $trace
20 $asTable
21 -o "$output"
22 ]]></command>
23 <inputs>
24 <param argument="-i" format="sbml" label="input SBML file: path to network used for computing scope, in sbml format." name="sbmlFilePath" optional="false" type="data" value=""/>
25 <param argument="-s" format="txt" label="input seeds file: tabulated file containing node of interest ids" name="seedsFilePath" optional="false" type="data" value=""/>
26 <param argument="-sc" format="txt" label="an optional file containing list of ubiquitous side compounds to be considered available by default but ignored during expansion" name="sideCompoundFile" optional="true" type="data" value=""/>
27 <param argument="-ssc" checked="false" falsevalue="" label="show side compounds in output network" name="includeSides" truevalue="-ssc" type="boolean" value="false"/>
28 <param argument="-ir" format="txt" label="an optional file containing list of reaction to ignore (forbid inclusion in scope" name="reactionToIgnoreFile" optional="true" type="data" value=""/>
29 <param argument="-t" checked="false" falsevalue="" label="trace inclusion step index for each node in output" name="trace" truevalue="-t" type="boolean" value="false"/>
30 <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/>
31 </inputs>
32 <outputs>
33 <data format="gml" name="output"/>
34 </outputs>
35 <tests>
36 <test>
37 <param name="sbmlFilePath" value="toy_model.xml"/>
38 <param name="seedsFilePath" value="seeds.txt"/>
39 <param name="sideCompoundFile" value="sides.txt"/>
40 <output ftype="gml" name="output">
41 <assert_contents>
42 <has_line_matching expression=".*node.*" n="9"/>
43 <has_line_matching expression=".*edge.*" n="11"/>
44 </assert_contents>
45 </output>
46 </test>
47 </tests>
48 <help><![CDATA[Perform a network expansion from a set of compound seeds to create a scope network
49 The scope of a set of compounds (seed) refer to the maximal metabolic network that can be extended from them,where the extension process consist of adding a reaction to the network if and only if all of its substrates are either a seed or a product of a previously added reaction
50 For more information, see Handorf, Ebenhöh and Heinrich (2005). *Expanding metabolic networks: scopes of compounds, robustness, and evolution.* Journal of molecular evolution, 61(4), 498-512. (https://doi.org/10.1007/s00239-005-0027-1)]]></help>
51 <citations/>
52 </tool>