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comparison hhsearch.xml @ 0:0dd6880ff950 draft

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"planemo upload commit 2ce78baac81e5fc7df43ca3ec81a3c51fdb98003"
author guerler
date Tue, 23 Mar 2021 21:38:01 +0000
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1 <tool id="hhsearch" name="HHsearch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description>detecting remote homologues of proteins</description>
3 <macros>
4 <token name="@TOOL_VERSION@">3.2.0</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 <xml name="ffindex_single_inputs">
7 <param name="ffdata" type="data" format="ffdata" label="PDB Database" help="Database Data file." />
8 <param name="ffindex" type="data" format="ffindex" label="PDB Database Index" help="Database Index file." />
9 </xml>
10 </macros>
11 <requirements>
12 <requirement type="package" version="@TOOL_VERSION@">hhsuite</requirement>
13 </requirements>
14 <command detect_errors="exit_code"><![CDATA[
15 #if $db_source.db_source_selector == 'indexed':
16 ln -s '${db_source.ffindex.fields.path}.ffdata' hhdb_hhm.ffdata &&
17 ln -s '${db_source.ffindex.fields.path}.ffindex' hhdb_hhm.ffindex &&
18 #else
19 ln -s '$db_source.ffdata' hhdb_hhm.ffdata &&
20 ln -s '$db_source.ffindex' hhdb_hhm.ffindex &&
21 #end if
22
23 #if $db_source_cs219.db_source_selector == 'indexed':
24 ln -s '${db_source_cs219.ffindex.fields.path}.ffdata' hhdb_cs219.ffdata &&
25 ln -s '${db_source_cs219.ffindex.fields.path}.ffindex' hhdb_cs219.ffindex &&
26 #else
27 ln -s '$db_source_cs219.ffdata' hhdb_cs219.ffdata &&
28 ln -s '$db_source_cs219.ffindex' hhdb_cs219.ffindex &&
29 #end if
30
31 $method
32 -cpu \${GALAXY_SLOTS:-1}
33 -e '$e'
34 -i '$i'
35 -d hhdb
36 -o '$output'
37 ]]> </command>
38 <inputs>
39 <param argument="--i" type="data" format="fasta,hmm3" label="Query Sequence" help="Single sequence or multiple sequence alignment (MSA)
40 in FASTA format, or HMM in hhm3 format." />
41 <param name="method" type="select" display="radio" label="Search Method" help="Select a search method. See help below for more information.">
42 <option value="hhsearch" selected="true">HHsearch</option>
43 <option value="hhblits">HHblits</option>
44 </param>
45 <conditional name="db_source">
46 <param name="db_source_selector" type="select" label="Custom or built-in HHM index" help="Built-ins have been indexed using ffindex">
47 <option value="indexed" selected="true">Use a built-in index</option>
48 <option value="history">Use a HHM index from history</option>
49 </param>
50 <when value="indexed">
51 <param name="ffindex" type="select" label="Select ffindex" help="">
52 <options from_data_table="ffindex_indices">
53 <filter type="sort_by" column="0" />
54 <filter type="static_value" column="3" value="hhm" />
55 <validator type="no_options" message="No indices are available" />
56 </options>
57 </param>
58 </when>
59 <when value="history">
60 <expand macro="ffindex_single_inputs" />
61 </when>
62 </conditional>
63
64 <conditional name="db_source_cs219">
65 <param name="db_source_selector" type="select" label="Custom or built-in cs219 index" help="Built-ins have been indexed using ffindex">
66 <option value="indexed" selected="true">Use a built-in index</option>
67 <option value="history">Use a cs219 index from history</option>
68 </param>
69 <when value="indexed">
70 <param name="ffindex" type="select" label="Select ffindex" help="">
71 <options from_data_table="ffindex_indices">
72 <filter type="sort_by" column="0" />
73 <filter type="static_value" column="3" value="cs219" />
74 <validator type="no_options" message="No indices are available" />
75 </options>
76 </param>
77 </when>
78 <when value="history">
79 <expand macro="ffindex_single_inputs" />
80 </when>
81 </conditional>
82 <param name="e" type="float" value="0.001" min="0" max="1" label="E-value cutoff for inclusion in result alignment. (-e)" />
83 </inputs>
84 <outputs>
85 <data format="hhr" name="output" />
86 </outputs>
87 <tests>
88 <test>
89 <param name="method" value="hhblits" />
90 <param name="i" value="6VYB_A.fasta" />
91 <conditional name="db_source">
92 <param name="db_source_selector" value="history" />
93 <param name="ffindex" value="dbCAN-fam-V8/dbCAN-fam-V8_hhm.ffindex" />
94 <param name="ffdata" value="dbCAN-fam-V8/dbCAN-fam-V8_hhm.ffdata" />
95 </conditional>
96 <conditional name="db_source_cs219">
97 <param name="db_source_selector" value="history" />
98 <param name="ffindex" value="dbCAN-fam-V8/dbCAN-fam-V8_cs219.ffindex" />
99 <param name="ffdata" value="dbCAN-fam-V8/dbCAN-fam-V8_cs219.ffdata" />
100 </conditional>
101 <output name="output" file="6VYB_A.hhr" lines_diff="4" ftype="hhr" />
102 </test>
103 <test>
104 <param name="method" value="hhblits" />
105 <param name="i" value="6VYB_A.fasta" />
106 <conditional name="db_source">
107 <param name="db_source_selector" value="indexed" />
108 <param name="ffindex" value="hmm_dbcan" />
109 </conditional>
110 <conditional name="db_source_cs219">
111 <param name="db_source_selector" value="indexed" />
112 <param name="ffindex" value="cs219_dbcan" />
113 </conditional>
114 <output name="output" file="6VYB_A.hhr" lines_diff="4" ftype="hhr" />
115 </test>
116 </tests>
117 <help><![CDATA[
118
119 **What it does**
120
121 HHsearch aligns a profile HMM against a database of target profile HMMs. The search first aligns the
122 query HMM with each of the target HMMs using the Viterbi dynamic programming algorithm, which finds the
123 alignment with the maximum score. The E-value for the target HMM is calculated from the Viterbi score.
124 Target HMMs that reach sufficient significance to be reported are realigned using the Maximum Accuracy algorithm (MAC).
125 This algorithm maximizes the expected number of correctly aligned pairs of residues minus a penalty between 0 and 1.
126 Values near 0 produce greedy, long, nearly global alignments, values above 0.3 result in shorter, local alignments.
127
128 HHblits is an accelerated version of HHsearch that is fast enough to perform iterative searches through millions of profile HMMs,
129 e.g. through the Uniclust profile HMM databases, generated by clustering the UniProt database into clusters of globally alignable sequences.
130 Analogously to PSI-BLAST and HMMER3, such iterative searches can be used to build MSAs by starting from a single query sequence.
131 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.
132
133 Download databases from: http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/
134 ]]> </help>
135 <citations>
136 <citation type="doi">10.1093/bioinformatics/bti125</citation>
137 </citations>
138 </tool>