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comparison data_manager/malt_index_builder.xml @ 0:d69ebf52c233 draft

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author greg
date Tue, 12 Oct 2021 14:15:35 +0000
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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">
2 <description></description>
3 <requirements>
4 <requirement type="package" version="0.53">malt</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 python '$__tool_directory__/malt_index_builder.py'
8 '${out_file}'
9 --fasta_filename '${all_fasta_source.fields.path}'
10 --fasta_dbkey '${all_fasta_source.fields.dbkey}'
11 --fasta_description '${all_fasta_source.fields.name}'
12 --sequence_type '${sequence_type}'
13 #if str($seed_setting_cond.seed_setting) == 'yes':
14 --shapes '${seed_setting_cond.shapes}'
15 --max_hits_per_seed $seed_setting_cond.max_hits_per_seed
16 --protein_reduct '${seed_setting_cond.protein_reduct}'
17 #end if
18 ]]></command>
19 <inputs>
20 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
21 <options from_data_table="all_fasta"/>
22 </param>
23 <param name="sequence_name" type="text" value="" label="Name of sequence" />
24 <param name="sequence_id" type="text" value="" label="ID for sequence" />
25 <param name="sequence_type" type="select" label="Specify whether the reference sequences are DNA or Protein sequences" help="Use the DNA setting For RNA sequences">
26 <option value="DNA" selected="true">DNA</option>
27 <option value="Protein">Protein</option>
28 </param>
29 <conditional name="seed_setting_cond">
30 <param name="seed_setting" type="select" label="Specify seed settings?">
31 <option selected="true" value="no">No</option>
32 <option value="yes">Yes</option>
33 </param>
34 <when value="no"/>
35 <when value="yes">
36 <param name="shapes" type="text" value="" label="Comma-separated list of seed shapes" help="See help text below">
37 <sanitizer invalid_char="">
38 <valid initial="string.printable">
39 <remove value="&apos;" />
40 </valid>
41 <mapping initial="none">
42 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
43 </mapping>
44 </sanitizer>
45 </param>
46 <param name="max_hits_per_seed" type="integer" value="1" min="1" label="Maximum number of hits per seed"/>
47 <param name="protein_reduct" type="select" label="Name or definition of protein alphabet reduction">
48 <option selected="true" value="DIAMOND_11">DIAMOND_11</option>
49 <option value="BLOSUM50_10">BLOSUM50_10</option>
50 <option value="BLOSUM50_11">BLOSUM50_11</option>
51 <option value="BLOSUM50_15">BLOSUM50_15</option>
52 <option value="BLOSUM50_4">BLOSUM50_4</option>
53 <option value="BLOSUM50_8">BLOSUM50_8</option>
54 <option value="GBMR4">GBMR4</option>
55 <option value="HSDM17">HSDM17</option>
56 <option value="MALT_10">MALT_10</option>
57 <option value="SDM12">SDM12</option>
58 <option value="UNREDUCED">UNREDUCED</option>
59 </param>
60 </when>
61 </conditional>
62 </inputs>
63 <outputs>
64 <data name="out_file" format="data_manager_json" />
65 </outputs>
66 <tests>
67 <test>
68 <param name="all_fasta_source" value="phiX174"/>
69 <output name="out_file" value="malt_index_builder.json"/>
70 </test>
71 </tests>
72 <help>
73 .. class:: infomark
74
75 **Notice:** Values for name, description, and id will be generated automatically if left blank.
76
77 **What it does**
78
79 Takes a reference sequence database (represented by a FastA file, possibly in gzip format) as input and produces an index that
80 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
81 alignment tool, then this MALT index builder tool must be provided with a number of mapping files that are used to map reference
82 sequences to taxonomic or functional classes or to locate genes in DNA reference sequences.
83
84 **Options**
85
86 * **Specify seed settings** - specify the settings for controlling how MALT uses its seed-and-extend approach based on “spaced seeds”.
87
88 * **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.
89 * **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.
90 * **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].
91 </help>
92 <citations>
93 <citation type="doi">https://doi.org/10.1101/050559</citation>
94 </citations>
95 </tool>