Mercurial > repos > guerler > hhsuite
comparison hhsearch.xml @ 5:3e4d88784254 draft
"planemo upload commit 3002402473e9f6dcdac5bfb4013cd2d81884a938-dirty"
| author | guerler |
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| date | Fri, 31 Jul 2020 23:16:55 -0400 |
| parents | |
| children | cec2aa4d6c0d |
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| 4:691d8f7c078c | 5:3e4d88784254 |
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| 1 <tool id="hhsearch" name="HHsearch" version="0.1.0" python_template_version="3.5"> | |
| 2 <description>detecting remote homologues from proteins</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="3.2.0">hhsuite</requirement> | |
| 5 </requirements> | |
| 6 <command detect_errors="exit_code"><![CDATA[ | |
| 7 link '$hhm_ffdata' hhdb_hhm.ffdata && | |
| 8 link '$hhm_ffindex' hhdb_hhm.ffindex && | |
| 9 link '$cs219_ffdata' hhdb_cs219.ffdata && | |
| 10 link '$cs219_ffindex' hhdb_cs219.ffindex && | |
| 11 $method -e '$e' -i '$input' -d hhdb -o '$output' | |
| 12 ]]></command> | |
| 13 <inputs> | |
| 14 <param format="data" name="input" type="data" label="Query Sequence" help="Single sequence or multiple sequence alignment (MSA) | |
| 15 in a3m, a2m, or FASTA format, or HMM in hhm format. (-i)"/> | |
| 16 <param format="txt" name="hhm_ffindex" type="data" label="HHM Index file" help="Database file ending with 'hhm.ffindex'."/> | |
| 17 <param format="data" name="hhm_ffdata" type="data" label="HHM Data file" help="Database file ending with 'hhm.ffdata'."/> | |
| 18 <param format="txt" name="cs219_ffindex" type="data" label="cs219 Index file" help="Database file ending with 'cs219.ffindex'."/> | |
| 19 <param format="data" name="cs219_ffdata" type="data" label="cs219 Data file" help="Database file ending with 'cs219.ffdata'."/> | |
| 20 <param name="method" type="select" display="radio" label="Search Method" help="Select a search method. See help below for more information."> | |
| 21 <option value="hhsearch" selected="true">HHsearch</option> | |
| 22 <option value="hhblits">HHblits</option> | |
| 23 </param> | |
| 24 <param name="e" type="float" label="E-value cutoff for inclusion in result alignment. (-e)" value="0.001" min="0" max="1"/> | |
| 25 </inputs> | |
| 26 <outputs> | |
| 27 <data format="txt" name="output" /> | |
| 28 </outputs> | |
| 29 <tests> | |
| 30 <test> | |
| 31 <param name="method" value="hhblits"/> | |
| 32 <param name="input" value="6VYB_A.fasta"/> | |
| 33 <param name="hhm_ffindex" value="dbCAN-fam-V8/dbCAN-fam-V8_hhm.ffindex"/> | |
| 34 <param name="hhm_ffdata" value="dbCAN-fam-V8/dbCAN-fam-V8_hhm.ffdata"/> | |
| 35 <param name="cs219_ffindex" value="dbCAN-fam-V8/dbCAN-fam-V8_cs219.ffindex"/> | |
| 36 <param name="cs219_ffdata" value="dbCAN-fam-V8/dbCAN-fam-V8_cs219.ffdata"/> | |
| 37 <output name="output" file="6VYB_A.hhr" lines_diff="4"/> | |
| 38 </test> | |
| 39 </tests> | |
| 40 <help><![CDATA[ | |
| 41 HHsearch aligns a profile HMM against a database of target profile HMMs. The search first aligns the | |
| 42 query HMM with each of the target HMMs using the Viterbi dynamic programming algorithm, which finds the | |
| 43 alignment with the maximum score. The E-value for the target HMM is calculated from the Viterbi score. | |
| 44 Target HMMs that reach sufficient significance to be reported are realigned using the Maximum Accuracy algorithm (MAC). | |
| 45 This algorithm maximizes the expected number of correctly aligned pairs of residues minus a penalty between 0 and 1. | |
| 46 Values near 0 produce greedy, long, nearly global alignments, values above 0.3 result in shorter, local alignments. | |
| 47 | |
| 48 HHblits is an accelerated version of HHsearch that is fast enough to perform iterative searches through millions of profile HMMs, | |
| 49 e.g. through the Uniclust profile HMM databases, generated by clustering the UniProt database into clusters of globally alignable sequences. | |
| 50 Analogously to PSI-BLAST and HMMER3, such iterative searches can be used to build MSAs by starting from a single query sequence. | |
| 51 Sequences from matches to profile HMMs below some E-value threshold (e.g. 10−3) are added to the query MSA for the next search iteration. | |
| 52 | |
| 53 Download databases from: http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/ | |
| 54 ]]></help> | |
| 55 <citations> | |
| 56 <citation type="bibtex"> | |
| 57 @misc{githubhh-suite, | |
| 58 author = {Soeding, Johannes}, | |
| 59 year = {2005}, | |
| 60 title = {Protein homology detection by HMM-HMM comparison}, | |
| 61 publisher = {Oxford University Press}, | |
| 62 journal = {Bioinformatics}, | |
| 63 url = {https://doi.org/10.1093/bioinformatics/bti125}, | |
| 64 }</citation> | |
| 65 </citations> | |
| 66 </tool> |