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comparison hhblits.xml @ 0:c4d9ea0ddd42 draft

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