Mercurial > repos > metexplore > met4j

annotate tools/networkAnalysis/ExtractSubBipNetwork/ExtractSubBipNetwork.xml @ 2:e69a78624877 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
1 <?xml version="1.0" encoding="UTF-8"?>
2
e69a78624877 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit cb957f5d5540a48293fe8487c0cfad78ab439d7c
metexplore
parents: 1
diff changeset
2 <tool id="met4j_ExtractSubBipNetwork" name="ExtractSubBipNetwork" version="1.0.1">
1
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
3 <description>Create a subnetwork from a GSMN in SBML format, and two files containing lists of compounds and/or reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.</description>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
4 <xrefs>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
5 <xref type="bio.tools">met4j</xref>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
6 </xrefs>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
7 <requirements>
2
e69a78624877 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit cb957f5d5540a48293fe8487c0cfad78ab439d7c
metexplore
parents: 1
diff changeset
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.0.1</container>
1
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
9 </requirements>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubBipNetwork -i "$inputPath"
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
11 -s "$sourcePath"
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
12 -t "$targetPath"
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
13 $undirected
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
14 $asTable
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
15 -sc "$sideCompoundFile"
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
16 #if str($blkdReactionFile) != 'None':
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
17 -br "$blkdReactionFile"
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
18 #end if
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
19 #if str($weightFile) != 'None':
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
20 -cw "$weightFile"
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
21 #end if
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
22 #if str($k):
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
23 -k "$k"
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
24 #end if
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
25 $st
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
26 -o "$outputPath"
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
27 ]]></command>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
28 <inputs>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
29 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
2
e69a78624877 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit cb957f5d5540a48293fe8487c0cfad78ab439d7c
metexplore
parents: 1
diff changeset
30 <param argument="-s" format="txt" label="input sources txt file" name="sourcePath" optional="false" type="data" value=""/>
e69a78624877 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit cb957f5d5540a48293fe8487c0cfad78ab439d7c
metexplore
parents: 1
diff changeset
31 <param argument="-t" format="txt" label="input targets txt file" name="targetPath" optional="false" type="data" value=""/>
1
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
32 <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
33 <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/>
2
e69a78624877 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit cb957f5d5540a48293fe8487c0cfad78ab439d7c
metexplore
parents: 1
diff changeset
34 <param argument="-sc" format="txt" label="a file containing list of side compounds to ignore" name="sideCompoundFile" optional="false" type="data" value=""/>
e69a78624877 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit cb957f5d5540a48293fe8487c0cfad78ab439d7c
metexplore
parents: 1
diff changeset
35 <param argument="-br" format="txt" label="a file containing list of blocked reactions to ignore" name="blkdReactionFile" optional="true" type="data" value=""/>
1
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
36 <param argument="-cw" format="tsv" label="an optional file containing weights for reactions pairs" name="weightFile" optional="true" type="data" value=""/>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
37 <param argument="-k" label="Extract k-shortest paths" name="k" optional="true" type="text" value="1">
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
38 <sanitizer invalid_char="_">
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
39 <valid initial="string.printable"/>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
40 </sanitizer>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
41 </param>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
42 <param argument="-st" checked="false" falsevalue="" label="Extract Steiner Tree" name="st" truevalue="-st" type="boolean" value="false"/>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
43 </inputs>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
44 <outputs>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
45 <data format="gml" name="outputPath"/>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
46 </outputs>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
47 <tests>
2
e69a78624877 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit cb957f5d5540a48293fe8487c0cfad78ab439d7c
metexplore
parents: 1
diff changeset
48 <test>
1
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
49 <param name="inputPath" value="toy_model.xml"/>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
50 <param name="sourcePath" value="seeds.txt"/>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
51 <param name="targetPath" value="targets.txt"/>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
52 <param name="sideCompoundFile" value="sc.txt"/>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
53 <output ftype="gml" name="outputPath">
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
54 <assert_contents>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
55 <has_line_matching expression=".*node.*" n="5"/>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
56 <has_line_matching expression=".*edge.*" n="4"/>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
57 </assert_contents>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
58 </output>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
59 </test>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
60 </tests>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
61 <help><![CDATA[Create a subnetwork from a GSMN in SBML format, and two files containing lists of compounds and/or reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
62 The subnetwork corresponds to part of the network that connects reactions and compounds from the first list to reactions and compounds from the second list.
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
63 Sources and targets list can have elements in common. The connecting part can be defined as the union of shortest or k-shortest paths between sources and targets, or the Steiner tree connecting them. Contrary to compound graph, bipartite graph often lacks weighting policy for edge relevance. In order to ensure appropriate network density, a list of side compounds and blocked reactions to ignore during path build must be provided. An optional edge weight file, if available, can also be used.]]></help>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
64 <citations/>
9b162ee6ff8e planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
metexplore
parents:
diff changeset
65 </tool>