Mercurial > repos > genouest > peptimapper_clustqualify

comparison clust_qualify.xml @ 0:1a673951d076 draft

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author genouest
date Fri, 10 Dec 2021 10:36:29 +0000
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1 <tool id="peptimapper_clustqualify" name="ClustQualify" version="2.0">
2 <description>annotates clusters according to gff annotation files</description>
3 <requirements>
4 <container type="docker">dockerprotim/peptimapper</container>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 mkdir 'repo' &&
8 unzip '${gffdir}' -d repo &&
9 LXQualify '$clustersfile' repo &&
10 mv '${clustersfile}.txt' '$clustersQualifResults'
11 ]]></command>
12 <inputs>
13 <param name="clustersfile" type="data" format="txt" label="Clusters file" help="Clusters file generated by PepMatch" />
14 <param name="gffdir" type="data" format="data" label="GFF files repository" help="zipped repository : for upload a zip repository into Galaxy, install before and use 'no_unzip.zip' datatype and select it into your upload form otherwise Galaxy decompress uploaded zip datatype file automatically"/>
15 </inputs>
16 <outputs>
17 <data format="txt" name="clustersQualifResults" label="${clustersfile.element_identifier}.qual"/>
18 </outputs>
19 <tests>
20 <test>
21 <param name="clustersfile" value="clustqualify/sample_01.mgf.3.5.tag.Nuc_genome.fasta.0.5.hit.2.2.5000.clust.txt"/>
22 <param name="gffdir" value="clustqualify/gff3_files_repository.zip"/>
23 <output name="clustersQualifResults" file="clustqualify/sample_01.mgf.3.5.tag.Nuc_genome.fasta.0.5.hit.2.2.5000.clust.qual.txt"/>
24 </test>
25 </tests>
26 <help><![CDATA[
27
28 **Description**
29
30 ClustQualify : run LXQualify from the "peptimapper" docker.
31 ClustQualify annotes clusters, generated from PepMatch, according to gff annotation files.
32
33 **Integrated by**
34
35 Laetitia Guillot Cloarec
36 PROTIM Biogenouest proteomics Core Facility, Rennes
37 May,2016
38
39 ]]></help>
40 <citations>
41 <citation type="bibtex">
42 @misc{renameTODO,
43 author = {Protim Core facility},
44 year = {2016},
45 title = {ClustQualify},
46 url = {protim.eu},
47 }
48 </citation>
49 </citations>
50 </tool>