Mercurial > repos > metexplore > met4j

annotate build/tools/ExtractPathways/ExtractPathways.xml @ 7:1436e9cde9c9 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 1d31a48bf8328b7a3ad9910971d24b9f453459c5
author metexplore
date Tue, 04 Jul 2023 10:21:26 +0000
parents 7a6f2380fc1d
children 1274e2a62479
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"?>
7
1436e9cde9c9 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents: 6
diff changeset
2 <tool id="met4j_ExtractPathways" name="ExtractPathways" version="1.4.0">
6
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
3 <description>Extract pathway(s) from GSMN</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>
7
1436e9cde9c9 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
metexplore
parents: 6
diff changeset
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.4.0</container>
6
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 attributes.ExtractPathways -i "$inputPath"
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
11 -p "$pathwayId"
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
12 -o "$outputPath"
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
13 ]]></command>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
14 <inputs>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
15 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
16 <param argument="-p" label="pathway identifiers, separated by &quot;+&quot; sign if more than one" name="pathwayId" optional="false" type="text" value="">
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
17 <sanitizer invalid_char="_">
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
18 <valid initial="string.printable"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
19 </sanitizer>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
20 </param>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
21 </inputs>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
22 <outputs>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
23 <data format="sbml" name="outputPath"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
24 </outputs>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
25 <tests>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
26 <test>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
27 <param name="inputPath" value="XF_network.sbml"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
28 <param name="pathwayId" value="Citric_Acid_Cycle+Folate_Metabolism+toto"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
29 <output ftype="sbml" name="outputPath">
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
30 <assert_contents>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
31 <is_valid_xml/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
32 <has_line_matching expression=".*&lt;reaction.*" n="17"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
33 <has_line_matching expression=".*groups:id=.*" n="2"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
34 </assert_contents>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
35 </output>
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 </tests>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
38 <help><![CDATA["Extract pathway(s) from GSMN: From a SBML file, Create a sub-network SBML file including only a selection of pathways]]></help>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
39 <citations/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
40 </tool>