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1 <tool id="data_manager_malt_index_builder" name="MALT index builder" tool_type="manage_data" version="0.5.3+galaxy0" profile="21.01">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="0.53">malt</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 python '$__tool_directory__/malt_index_builder.py'
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8 '${out_file}'
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9 --fasta_filename '${all_fasta_source.fields.path}'
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10 --fasta_dbkey '${all_fasta_source.fields.dbkey}'
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11 --fasta_description '${all_fasta_source.fields.name}'
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12 --sequence_type '${sequence_type}'
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13 #if str($protein_reduct_setting_cond.protein_reduct_setting) == 'yes':
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14 --protein_reduct '${protein_reduct_setting_cond.protein_reduct}'
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15 #end if
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16 #if str($seed_setting_cond.seed_setting) == 'yes':
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17 --shapes '${seed_setting_cond.shapes}'
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18 ## malt-build requires a string here.
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19 --max_hits_per_seed '${seed_setting_cond.max_hits_per_seed}'
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20 #end if
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21 ]]></command>
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22 <inputs>
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23 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
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24 <options from_data_table="all_fasta"/>
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25 </param>
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26 <param name="sequence_name" type="text" value="" label="Name of sequence"/>
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27 <param name="sequence_id" type="text" value="" label="ID for sequence"/>
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28 <param name="sequence_type" type="select" label="Reference sequences type" help="Use the DNA setting For RNA sequences">
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29 <option value="DNA" selected="true">DNA</option>
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30 <option value="Protein">Protein</option>
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31 </param>
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32 <conditional name="protein_reduct_setting_cond">
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33 <param name="protein_reduct_setting" type="select" label="Specify protein alphabet resuction?" help="Used only if the reference sequences are Protein sequences">
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34 <option selected="true" value="no">No</option>
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35 <option value="yes">Yes</option>
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36 </param>
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37 <when value="no"/>
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38 <when value="yes">
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39 <param name="protein_reduct" type="select" label="Name or definition of protein alphabet reduction">
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40 <option selected="true" value="DIAMOND_11">DIAMOND_11</option>
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41 <option value="BLOSUM50_10">BLOSUM50_10</option>
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42 <option value="BLOSUM50_11">BLOSUM50_11</option>
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43 <option value="BLOSUM50_15">BLOSUM50_15</option>
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44 <option value="BLOSUM50_4">BLOSUM50_4</option>
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45 <option value="BLOSUM50_8">BLOSUM50_8</option>
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46 <option value="GBMR4">GBMR4</option>
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47 <option value="HSDM17">HSDM17</option>
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48 <option value="MALT_10">MALT_10</option>
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49 <option value="SDM12">SDM12</option>
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50 <option value="UNREDUCED">UNREDUCED</option>
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51 </param>
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52 </when>
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53 </conditional>
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54 <conditional name="seed_setting_cond">
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55 <param name="seed_setting" type="select" label="Specify seed settings?">
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56 <option selected="true" value="no">No</option>
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57 <option value="yes">Yes</option>
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58 </param>
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59 <when value="no"/>
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60 <when value="yes">
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61 <param name="shapes" type="text" value="" label="Comma-separated list of seed shapes" help="See help text below">
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62 <sanitizer invalid_char="">
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63 <valid initial="string.printable">
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64 <remove value="'"/>
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65 </valid>
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66 <mapping initial="none">
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67 <add source="'" target="'"'"'"/>
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68 </mapping>
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69 </sanitizer>
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70 </param>
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71 <param name="max_hits_per_seed" type="integer" value="1" min="1" label="Maximum number of hits per seed"/>
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72 </when>
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73 </conditional>
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74 </inputs>
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75 <outputs>
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76 <data name="out_file" format="data_manager_json"/>
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77 </outputs>
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78 <tests>
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79 <test>
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80 <param name="all_fasta_source" value="phiX174"/>
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81 <param name="sequence_name" value="Pretty name for phiX174"/>
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82 <param name="sequence_id" value="phiX174-1"/>
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83 <output name="out_file" value="malt_index_builder1.json"/>
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84 </test>
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85 <test>
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86 <param name="all_fasta_source" value="phiX174"/>
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87 <param name="sequence_name" value="Pretty name for phiX174"/>
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88 <param name="sequence_id" value="phiX174-1"/>
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89 <param name="seed_setting" value="yes"/>
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90 <param name="shapes" value="111110111011110110111111"/>
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91 <output name="out_file" value="malt_index_builder1.json"/>
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92 </test>
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93 <test>
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94 <param name="all_fasta_source" value="phiX174"/>
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95 <param name="sequence_name" value="Pretty name for phiX174"/>
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96 <param name="sequence_id" value="phiX174-2"/>
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97 <param name="sequence_type" value="Protein"/>
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98 <param name="protein_reduct_setting" value="yes"/>
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99 <param name="protein_reduct" value="BLOSUM50_10"/>
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100 <output name="out_file" value="malt_index_builder2.json"/>
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101 </test>
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102 </tests>
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103 <help>
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104 .. class:: infomark
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105
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106 **Notice:** Values for Name and ID of sequence will be generated automatically if left blank.
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107
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108 **What it does**
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109
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110 Takes a reference sequence database (represented by a FastA file, possibly in gzip format) as input and produces an index that
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111 can be used by the malt tool as input. If MALT is to be used as a taxonomic and/or functional analysis tool as well as an
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112 alignment tool, then this MALT index builder tool must be provided with a number of mapping files that are used to map reference
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113 sequences to taxonomic or functional classes or to locate genes in DNA reference sequences.
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114
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115 **Options**
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116
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117 * **Specify seed settings** - specify the settings for controlling how MALT uses its seed-and-extend approach based on “spaced seeds”.
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118
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119 * **Shapes** - specify the seed shapes used. For DNA sequences, the default seed shape is: 111110111011110110111111. For protein sequences, by default MALT uses the following four shapes: 111101101110111, 1111000101011001111, 11101001001000100101111 and 11101001000010100010100111.
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120 * **Maximim hits per seed** - specify the maximum number of hits per seed - MALT uses this to calculate a maximum number of hits per hash value.
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121 * **Protein reduction** - specify the alphabet reduction in the case of protein reference sequences. By default, MALT reduces amino acids to 8 different letters, grouped as follows: [LVIMC] [AG] [ST] [P] [FYW] [EDNQ] [KR] [H].
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122 </help>
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123 <citations>
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124 <citation type="doi">https://doi.org/10.1101/050559</citation>
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125 </citations>
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126 </tool>
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