annotate 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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
1 <?xml version="1.0" encoding="UTF-8"?>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
2 <tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="1.3.0">
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
3 <description>Perform a network expansion from a set of compound seeds to create a scope network</description>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
4 <xrefs>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
5 <xref type="bio.tools">met4j</xref>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
6 </xrefs>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
7 <requirements>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
9 </requirements>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ScopeNetwork -i "$sbmlFilePath"
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
11 -s "$seedsFilePath"
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
12 #if str($sideCompoundFile) != 'None':
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
13 -sc "$sideCompoundFile"
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
14 #end if
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
15 $includeSides
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
16 #if str($reactionToIgnoreFile) != 'None':
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
17 -ir "$reactionToIgnoreFile"
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
18 #end if
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
19 $trace
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
20 $asTable
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
21 -o "$output"
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
22 ]]></command>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
23 <inputs>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
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=""/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
25 <param argument="-s" format="txt" label="input seeds file: tabulated file containing node of interest ids" name="seedsFilePath" optional="false" type="data" value=""/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
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=""/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
27 <param argument="-ssc" checked="false" falsevalue="" label="show side compounds in output network" name="includeSides" truevalue="-ssc" type="boolean" value="false"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
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=""/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
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"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
30 <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
31 </inputs>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
32 <outputs>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
33 <data format="gml" name="output"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
34 </outputs>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
35 <tests>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
36 <test>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
37 <param name="sbmlFilePath" value="toy_model.xml"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
38 <param name="seedsFilePath" value="seeds.txt"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
39 <param name="sideCompoundFile" value="sides.txt"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
40 <output ftype="gml" name="output">
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
41 <assert_contents>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
42 <has_line_matching expression=".*node.*" n="9"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
43 <has_line_matching expression=".*edge.*" n="11"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
44 </assert_contents>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
45 </output>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
46 </test>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
47 </tests>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
48 <help><![CDATA[Perform a network expansion from a set of compound seeds to create a scope network
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
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
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
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>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
51 <citations/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
52 </tool>