Mercurial > repos > metexplore > met4j

annotate build/tools/GetModelProteome/GetModelProteome.xml @ 8:1274e2a62479 draft default tip

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 e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
author metexplore
date Wed, 26 Jul 2023 15:33:45 +0000
parents 1436e9cde9c9
children
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"?>
8
1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
metexplore
parents: 7
diff changeset
2 <tool id="met4j_GetModelProteome" name="GetModelProteome" version="1.5.0">
6
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
3 <description>Get proteome in fasta format of a model present in BIGG</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>
8
1274e2a62479 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit e34acf0f51cafcf6ae7c97b4feb3188a39f17c32
metexplore
parents: 7
diff changeset
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.5.0</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 bigg.GetModelProteome -m "$modelId"
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
11 -o "$outputFile"
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
12 ]]></command>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
13 <inputs>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
14 <param argument="-m" label="[ex: iMM904] id of the BIGG model" name="modelId" optional="false" type="text" value="iMM904">
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
15 <sanitizer invalid_char="_">
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
16 <valid initial="string.printable"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
17 </sanitizer>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
18 </param>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
19 </inputs>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
20 <outputs>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
21 <data format="fasta" name="outputFile"/>
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 <tests>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
24 <test maxseconds="120">
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
25 <param name="modelId" value="e_coli_core"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
26 <output ftype="fasta" name="outputFile">
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
27 <assert_contents>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
28 <has_line_matching expression=".*name=.*" n="136"/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
29 </assert_contents>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
30 </output>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
31 </test>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
32 </tests>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
33 <help><![CDATA[Get proteome in fasta format of a model present in BIGG]]></help>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
34 <citations/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
metexplore
parents:
diff changeset
35 </tool>