Mercurial > repos > metexplore > met4j

annotate tools/attributes/GetGenesFromReactions/GetGenesFromReactions.xml @ 5:35c9abcd8934 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 8577c4cd3ad279c5e97f48f822e041c6b0d90598
author metexplore
date Thu, 12 Jan 2023 13:45:13 +0000
parents ae4c301919c4
children 7a6f2380fc1d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
1 <?xml version="1.0" encoding="UTF-8"?>
5
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents: 4
diff changeset
2 <tool id="met4j_GetGenesFromReactions" name="GetGenesFromReactions" version="1.2.1">
3
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
3 <description>Get gene lists from a list of reactions and a GSMN.</description>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
4 <xrefs>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
5 <xref type="bio.tools">met4j</xref>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
6 </xrefs>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
7 <requirements>
5
35c9abcd8934 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 8577c4cd3ad279c5e97f48f822e041c6b0d90598
metexplore
parents: 4
diff changeset
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.1</container>
3
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
9 </requirements>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.GetGenesFromReactions -i "$sbml"
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
11 -r "$reactionFile"
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
12 #if str($sep):
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
13 -sep "$sep"
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
14 #end if
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
15 $hasHeader
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
16 #if str($i) != 'nan':
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
17 -col "$i"
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
18 #end if
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
19 -o "$outputFile"
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
20 ]]></command>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
21 <inputs>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
22 <param argument="-i" format="sbml" label="Input SBML file" name="sbml" optional="false" type="data" value=""/>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
23 <param argument="-r" format="tsv" label="Input Reaction file" name="reactionFile" optional="false" type="data" value=""/>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
24 <param argument="-sep" label="Separator in reaction file" name="sep" optional="true" type="text" value="&#9;">
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
25 <sanitizer invalid_char="_">
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
26 <valid initial="string.printable"/>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
27 </sanitizer>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
28 </param>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
29 <param argument="-header" checked="false" falsevalue="" label="Skip reaction file header" name="hasHeader" truevalue="-header" type="boolean" value="false"/>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
30 <param argument="-col" label="Column number in reaction file (first as 1)" name="i" optional="true" type="integer" value="1"/>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
31 </inputs>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
32 <outputs>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
33 <data format="tsv" name="outputFile"/>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
34 </outputs>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
35 <tests>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
36 <test>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
37 <param name="sbml" value="XF_network.sbml"/>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
38 <param name="reactionFile" value="XF_network_R_Seed.tab"/>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
39 <output ftype="tsv" name="outputFile">
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
40 <assert_contents>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
41 <has_n_lines n="2"/>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
42 <has_line_matching expression="R_GLUN.*XFCFBP8418_026750" n="1"/>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
43 <has_line_matching expression="R_ACGS.*XFCFBP8418_025260" n="1"/>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
44 </assert_contents>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
45 </output>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
46 </test>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
47 </tests>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
48 <help><![CDATA[Get associated gene list from a list of reactions and a GSMN. Parse GSMN GPR annotations and output a tab-separated file with one row per gene, associated reaction identifiers from input file in first column, gene identifiers in second column.]]></help>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
49 <citations/>
6bd9aad9626d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit a078bf88575dac3d09462252eae92c24f34d0414
metexplore
parents:
diff changeset
50 </tool>