Mercurial > repos > genouest > clustqualify

annotate clust_qualify.xml @ 0:aef012f20f22 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
author genouest
date Fri, 10 Dec 2021 10:26:25 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
1 <tool id="ClustQualify" name="ClustQualify" version="2.0">
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
2 <description>annotates clusters according to gff annotation files</description>
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
3 <requirements>
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
4 <container type="docker">dockerprotim/peptimapper</container>
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
5 </requirements>
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
6 <command detect_errors="exit_code"><![CDATA[
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
7 mkdir 'repo' &&
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
8 unzip '${gffdir}' -d repo &&
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
9 LXQualify '$clustersfile' repo &&
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
10 mv '${clustersfile}.txt' '$clustersQualifResults'
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
11 ]]></command>
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
12 <inputs>
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
13 <param name="clustersfile" type="data" format="txt" label="Clusters file" help="Clusters file generated by PepMatch" />
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
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"/>
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
15 </inputs>
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
16 <outputs>
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
17 <data format="txt" name="clustersQualifResults" label="${clustersfile.element_identifier}.qual"/>
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
18 </outputs>
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
19 <tests>
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
20 <test>
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
21 <param name="clustersfile" value="clustqualify/sample_01.mgf.3.5.tag.Nuc_genome.fasta.0.5.hit.2.2.5000.clust.txt"/>
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
22 <param name="gffdir" value="clustqualify/gff3_files_repository.zip"/>
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
23 <output name="clustersQualifResults" file="clustqualify/sample_01.mgf.3.5.tag.Nuc_genome.fasta.0.5.hit.2.2.5000.clust.qual.txt"/>
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
24 </test>
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
25 </tests>
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
26 <help><![CDATA[
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
27
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
28 **Description**
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
29
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
30 ClustQualify : run LXQualify from the "peptimapper" docker.
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
31 ClustQualify annotes clusters, generated from PepMatch, according to gff annotation files.
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
32
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
33 **Integrated by**
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
34
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
35 Laetitia Guillot Cloarec
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
36 PROTIM Biogenouest proteomics Core Facility, Rennes
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
37 May,2016
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
38
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
39 ]]></help>
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
40 <citations>
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
41 <citation type="bibtex">
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
42 @misc{renameTODO,
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
43 author = {Protim Core facility},
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
44 year = {2016},
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
45 title = {ClustQualify},
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
46 url = {protim.eu},
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
47 }
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
48 </citation>
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
49 </citations>
aef012f20f22 "planemo upload commit 75205d9b1b403cac3cf06b4d25148483181ed708"
genouest
parents:
diff changeset
50 </tool>