Mercurial > repos > guerler > hhsuite

annotate hhblits.xml @ 0:c4d9ea0ddd42 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
author guerler
date Mon, 27 Jul 2020 04:37:03 -0400
parents
children a6b54ca2bded
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
1 <tool id="hhblits" name="HH-blits itererative protein sequence searching" version="0.1.0" python_template_version="3.5">
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
2 <requirements>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
3 <requirement type="package" version="3.2.0">hhsuite</requirement>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
4 </requirements>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
5 <command detect_errors="exit_code"><![CDATA[
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
6 link $hhm_ffdata hhdb_hhm.ffdata &&
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
7 link $hhm_ffindex hhdb_hhm.ffindex &&
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
8 link $cs219_ffdata hhdb_cs219.ffdata &&
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
9 link $cs219_ffindex hhdb_cs219.ffindex &&
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
10 hhblits -n $n -e $e -i $input -d hhdb -o $output
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
11 ]]></command>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
12 <inputs>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
13 <param format="data" name="input" type="data" label="Query Sequence" help="Single sequence or multiple sequence alignment (MSA)
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
14 in a3m, a2m, or FASTA format, or HMM in hhm format (-i)"/>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
15 <param format="data" name="hhm_ffindex" type="data" label="HHM Index file" help="Database file ending with 'hhm.ffindex'"/>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
16 <param format="data" name="hhm_ffdata" type="data" label="HHM Data file" help="Database file ending with 'hhm.ffdata'"/>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
17 <param format="data" name="cs219_ffindex" type="data" label="cs219 Index file" help="Database file ending with 'cs219.ffindex'"/>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
18 <param format="data" name="cs219_ffdata" type="data" label="cs219 Data file" help="Database file ending with 'cs219.ffdata'"/>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
19 <param name="n" type="integer" label="Number of Iterations (-n)" value="2" min="1" max="8"/>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
20 <param name="e" type="float" label="E-value cutoff for inclusion in result alignment (-e)" value="0.001" min="0" max="1"/>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
21 </inputs>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
22 <outputs>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
23 <data format="fasta" name="output" />
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
24 </outputs>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
25 <tests>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
26 <test>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
27 <param name="input" value="6VYB_A.fasta"/>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
28 <param name="hhm_ffindex" value="dbCAN-fam-V8/dbCAN-fam-V8_hhm.ffindex"/>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
29 <param name="hhm_ffdata" value="dbCAN-fam-V8/dbCAN-fam-V8_hhm.ffdata"/>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
30 <param name="cs219_ffindex" value="dbCAN-fam-V8/dbCAN-fam-V8_cs219.ffindex"/>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
31 <param name="cs219_ffdata" value="dbCAN-fam-V8/dbCAN-fam-V8_cs219.ffdata"/>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
32 <output name="output" file="6VYB_A.hhr" lines_diff="4"/>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
33 </test>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
34 </tests>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
35 <help><![CDATA[
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
36 HMM-HMM-based lightning-fast iterative sequence search
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
37 HHblits is a sensitive, general-purpose, iterative sequence search tool that represents
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
38 both query and database sequences by HMMs. You can search HHblits databases starting
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
39 with a single query sequence, a multiple sequence alignment (MSA), or an HMM. HHblits
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
40 prints out a ranked list of database HMMs/MSAs and can also generate an MSA by merging
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
41 the significant database HMMs/MSAs onto the query MSA.
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
42
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
43 Steinegger M, Meier M, Mirdita M, Vöhringer H, Haunsberger S J, and Söding J (2019)
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
44 HH-suite3 for fast remote homology detection and deep protein annotation.
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
45 bioRxiv, 560029. doi:10.1101/560029
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
46 (c) The HH-suite development team
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
47
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
48 Download databases from <http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/>.
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
49 ]]></help>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
50 <citations>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
51 <citation type="bibtex">
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
52 @misc{githubhh-suite,
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
53 author = {Soeding, Johannes},
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
54 year = {2005},
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
55 title = {Protein homology detection by HMM-HMM comparison},
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
56 publisher = {Oxford University Press},
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
57 journal = {Bioinformatics},
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
58 url = {https://doi.org/10.1093/bioinformatics/bti125},
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
59 }</citation>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
60 </citations>
c4d9ea0ddd42 "planemo upload commit d12c32a45bcd441307e632fca6d9af7d60289d44-dirty"
guerler
parents:
diff changeset
61 </tool>