Mercurial > repos > genouest > peptimapper_clustqualify

annotate clust_qualify.xml @ 1:d913a2af45dc draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit bbcbc29ef60120ea945879874ca92fb098dda8bf"
author genouest
date Mon, 13 Dec 2021 14:13:08 +0000
parents 1a673951d076
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
1 <tool id="peptimapper_clustqualify" name="ClustQualify" version="2.0">
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
2 <description>annotates clusters according to gff annotation files</description>
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
3 <requirements>
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
4 <container type="docker">dockerprotim/peptimapper</container>
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
5 </requirements>
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
6 <command detect_errors="exit_code"><![CDATA[
1
d913a2af45dc "planemo upload commit bbcbc29ef60120ea945879874ca92fb098dda8bf"
genouest
parents: 0
diff changeset
7 ln -s '$clustersfile' 'in.clusters' &&
0
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
8 mkdir 'repo' &&
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
9 unzip '${gffdir}' -d repo &&
1
d913a2af45dc "planemo upload commit bbcbc29ef60120ea945879874ca92fb098dda8bf"
genouest
parents: 0
diff changeset
10 LXQualify 'in.clusters' repo &&
d913a2af45dc "planemo upload commit bbcbc29ef60120ea945879874ca92fb098dda8bf"
genouest
parents: 0
diff changeset
11 mv 'in.clusters.txt' '$clustersQualifResults'
0
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
12 ]]></command>
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
13 <inputs>
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
14 <param name="clustersfile" type="data" format="txt" label="Clusters file" help="Clusters file generated by PepMatch" />
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
15 <param name="gffdir" type="data" format="data" label="GFF files repository" help="zipped repository : for upload a zip repository into Galaxy, install before and use 'no_unzip.zip' datatype and select it into your upload form otherwise Galaxy decompress uploaded zip datatype file automatically"/>
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
16 </inputs>
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
17 <outputs>
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
18 <data format="txt" name="clustersQualifResults" label="${clustersfile.element_identifier}.qual"/>
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
19 </outputs>
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
20 <tests>
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
21 <test>
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
22 <param name="clustersfile" value="clustqualify/sample_01.mgf.3.5.tag.Nuc_genome.fasta.0.5.hit.2.2.5000.clust.txt"/>
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
23 <param name="gffdir" value="clustqualify/gff3_files_repository.zip"/>
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
24 <output name="clustersQualifResults" file="clustqualify/sample_01.mgf.3.5.tag.Nuc_genome.fasta.0.5.hit.2.2.5000.clust.qual.txt"/>
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
25 </test>
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
26 </tests>
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
27 <help><![CDATA[
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
28
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
29 **Description**
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
30
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
31 ClustQualify : run LXQualify from the "peptimapper" docker.
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
32 ClustQualify annotes clusters, generated from PepMatch, according to gff annotation files.
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
33
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
34 **Integrated by**
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
35
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
36 Laetitia Guillot Cloarec
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
37 PROTIM Biogenouest proteomics Core Facility, Rennes
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
38 May,2016
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
39
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
40 ]]></help>
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
41 <citations>
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
42 <citation type="bibtex">
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
43 @misc{renameTODO,
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
44 author = {Protim Core facility},
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
45 year = {2016},
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
46 title = {ClustQualify},
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
47 url = {protim.eu},
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
48 }
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
49 </citation>
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
50 </citations>
1a673951d076 "planemo upload commit 9db7cd910ae897f1d9ea968be0178cc2faf305d4"
genouest
parents:
diff changeset
51 </tool>