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annotate hhsearch.xml @ 0:0dd6880ff950 draft

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"planemo upload commit 2ce78baac81e5fc7df43ca3ec81a3c51fdb98003"
author guerler
date Tue, 23 Mar 2021 21:38:01 +0000
parents
children 589e4d51bda4
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1 <tool id="hhsearch" name="HHsearch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>detecting remote homologues of proteins</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">3.2.0</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 <xml name="ffindex_single_inputs">
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7 <param name="ffdata" type="data" format="ffdata" label="PDB Database" help="Database Data file." />
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8 <param name="ffindex" type="data" format="ffindex" label="PDB Database Index" help="Database Index file." />
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9 </xml>
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10 </macros>
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11 <requirements>
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12 <requirement type="package" version="@TOOL_VERSION@">hhsuite</requirement>
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13 </requirements>
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14 <command detect_errors="exit_code"><![CDATA[
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15 #if $db_source.db_source_selector == 'indexed':
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16 ln -s '${db_source.ffindex.fields.path}.ffdata' hhdb_hhm.ffdata &&
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17 ln -s '${db_source.ffindex.fields.path}.ffindex' hhdb_hhm.ffindex &&
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18 #else
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19 ln -s '$db_source.ffdata' hhdb_hhm.ffdata &&
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20 ln -s '$db_source.ffindex' hhdb_hhm.ffindex &&
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21 #end if
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22
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23 #if $db_source_cs219.db_source_selector == 'indexed':
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24 ln -s '${db_source_cs219.ffindex.fields.path}.ffdata' hhdb_cs219.ffdata &&
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25 ln -s '${db_source_cs219.ffindex.fields.path}.ffindex' hhdb_cs219.ffindex &&
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26 #else
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27 ln -s '$db_source_cs219.ffdata' hhdb_cs219.ffdata &&
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28 ln -s '$db_source_cs219.ffindex' hhdb_cs219.ffindex &&
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29 #end if
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30
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31 $method
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32 -cpu \${GALAXY_SLOTS:-1}
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33 -e '$e'
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34 -i '$i'
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35 -d hhdb
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36 -o '$output'
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37 ]]> </command>
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38 <inputs>
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39 <param argument="--i" type="data" format="fasta,hmm3" label="Query Sequence" help="Single sequence or multiple sequence alignment (MSA)
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40 in FASTA format, or HMM in hhm3 format." />
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41 <param name="method" type="select" display="radio" label="Search Method" help="Select a search method. See help below for more information.">
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42 <option value="hhsearch" selected="true">HHsearch</option>
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43 <option value="hhblits">HHblits</option>
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44 </param>
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45 <conditional name="db_source">
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46 <param name="db_source_selector" type="select" label="Custom or built-in HHM index" help="Built-ins have been indexed using ffindex">
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47 <option value="indexed" selected="true">Use a built-in index</option>
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48 <option value="history">Use a HHM index from history</option>
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49 </param>
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50 <when value="indexed">
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51 <param name="ffindex" type="select" label="Select ffindex" help="">
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52 <options from_data_table="ffindex_indices">
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53 <filter type="sort_by" column="0" />
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54 <filter type="static_value" column="3" value="hhm" />
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55 <validator type="no_options" message="No indices are available" />
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56 </options>
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57 </param>
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58 </when>
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59 <when value="history">
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60 <expand macro="ffindex_single_inputs" />
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61 </when>
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62 </conditional>
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63
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64 <conditional name="db_source_cs219">
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65 <param name="db_source_selector" type="select" label="Custom or built-in cs219 index" help="Built-ins have been indexed using ffindex">
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66 <option value="indexed" selected="true">Use a built-in index</option>
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67 <option value="history">Use a cs219 index from history</option>
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68 </param>
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69 <when value="indexed">
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70 <param name="ffindex" type="select" label="Select ffindex" help="">
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71 <options from_data_table="ffindex_indices">
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72 <filter type="sort_by" column="0" />
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73 <filter type="static_value" column="3" value="cs219" />
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74 <validator type="no_options" message="No indices are available" />
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75 </options>
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76 </param>
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77 </when>
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78 <when value="history">
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79 <expand macro="ffindex_single_inputs" />
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80 </when>
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81 </conditional>
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82 <param name="e" type="float" value="0.001" min="0" max="1" label="E-value cutoff for inclusion in result alignment. (-e)" />
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83 </inputs>
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84 <outputs>
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85 <data format="hhr" name="output" />
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86 </outputs>
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87 <tests>
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88 <test>
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89 <param name="method" value="hhblits" />
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90 <param name="i" value="6VYB_A.fasta" />
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91 <conditional name="db_source">
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92 <param name="db_source_selector" value="history" />
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93 <param name="ffindex" value="dbCAN-fam-V8/dbCAN-fam-V8_hhm.ffindex" />
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94 <param name="ffdata" value="dbCAN-fam-V8/dbCAN-fam-V8_hhm.ffdata" />
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95 </conditional>
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96 <conditional name="db_source_cs219">
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97 <param name="db_source_selector" value="history" />
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98 <param name="ffindex" value="dbCAN-fam-V8/dbCAN-fam-V8_cs219.ffindex" />
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99 <param name="ffdata" value="dbCAN-fam-V8/dbCAN-fam-V8_cs219.ffdata" />
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100 </conditional>
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101 <output name="output" file="6VYB_A.hhr" lines_diff="4" ftype="hhr" />
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102 </test>
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103 <test>
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104 <param name="method" value="hhblits" />
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105 <param name="i" value="6VYB_A.fasta" />
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106 <conditional name="db_source">
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107 <param name="db_source_selector" value="indexed" />
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108 <param name="ffindex" value="hmm_dbcan" />
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109 </conditional>
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110 <conditional name="db_source_cs219">
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111 <param name="db_source_selector" value="indexed" />
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112 <param name="ffindex" value="cs219_dbcan" />
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113 </conditional>
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114 <output name="output" file="6VYB_A.hhr" lines_diff="4" ftype="hhr" />
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115 </test>
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116 </tests>
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117 <help><![CDATA[
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118
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119 **What it does**
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120
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121 HHsearch aligns a profile HMM against a database of target profile HMMs. The search first aligns the
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122 query HMM with each of the target HMMs using the Viterbi dynamic programming algorithm, which finds the
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123 alignment with the maximum score. The E-value for the target HMM is calculated from the Viterbi score.
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124 Target HMMs that reach sufficient significance to be reported are realigned using the Maximum Accuracy algorithm (MAC).
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125 This algorithm maximizes the expected number of correctly aligned pairs of residues minus a penalty between 0 and 1.
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126 Values near 0 produce greedy, long, nearly global alignments, values above 0.3 result in shorter, local alignments.
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127
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128 HHblits is an accelerated version of HHsearch that is fast enough to perform iterative searches through millions of profile HMMs,
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129 e.g. through the Uniclust profile HMM databases, generated by clustering the UniProt database into clusters of globally alignable sequences.
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130 Analogously to PSI-BLAST and HMMER3, such iterative searches can be used to build MSAs by starting from a single query sequence.
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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.
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132
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133 Download databases from: http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/
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134 ]]> </help>
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135 <citations>
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136 <citation type="doi">10.1093/bioinformatics/bti125</citation>
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137 </citations>
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138 </tool>