[2] | 1 | <tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.1"> |
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| 2 | <description>Search nucleotide database with nucleotide query sequence(s)</description> |
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| 3 | <command> |
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| 4 | ## The command is a Cheetah template which allows some Python based syntax. |
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| 5 | ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces |
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| 6 | blastn |
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| 7 | -query "$query" |
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| 8 | #if $db_opts.db_opts_selector == "db": |
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| 9 | -db "$db_opts.database" |
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| 10 | #else: |
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| 11 | -subject "$db_opts.subject" |
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| 12 | #end if |
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| 13 | -task $blast_type |
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| 14 | -evalue $evalue_cutoff |
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| 15 | $adv_opts.filter_query |
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| 16 | $adv_opts.strand |
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| 17 | -out $output1 |
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| 18 | $out_format |
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| 19 | -num_threads 8 |
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| 20 | ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string |
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| 21 | ## Note -max_target_seqs overrides -num_descriptions and -num_alignments |
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| 22 | #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): |
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| 23 | -max_target_seqs $adv_opts.max_hits |
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| 24 | #end if |
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| 25 | #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): |
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| 26 | -word_size $adv_opts.word_size |
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| 27 | #end if |
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| 28 | $adv_opts.ungapped |
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| 29 | </command> |
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| 30 | <inputs> |
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| 31 | <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> |
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| 32 | <conditional name="db_opts"> |
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| 33 | <param name="db_opts_selector" type="select" label="Subject database/sequences"> |
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| 34 | <option value="db" selected="True">BLAST Database</option> |
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| 35 | <option value="file">FASTA file</option> |
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| 36 | </param> |
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| 37 | <when value="db"> |
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| 38 | <param name="database" type="select" label="Nucleotide BLAST database"> |
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| 39 | <options from_file="blastdb.loc"> |
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| 40 | <column name="name" index="0"/> |
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| 41 | <column name="value" index="1"/> |
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| 42 | </options> |
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| 43 | </param> |
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| 44 | <param name="subject" type="hidden" value="" /> |
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| 45 | </when> |
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| 46 | <when value="file"> |
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| 47 | <param name="database" type="hidden" value="" /> |
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| 48 | <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> |
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| 49 | </when> |
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| 50 | </conditional> |
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| 51 | <param name="blast_type" type="select" display="radio" label="Type of BLAST"> |
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| 52 | <option value="megablast">megablast</option> |
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| 53 | <option value="blastn">blastn</option> |
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| 54 | <option value="blastn-short">blastn-short</option> |
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| 55 | <option value="dc-megablast">dc-megablast</option> |
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| 56 | <!-- Using BLAST 2.2.24+ this gives an error: |
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| 57 | BLAST engine error: Program type 'vecscreen' not supported |
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| 58 | <option value="vecscreen">vecscreen</option> |
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| 59 | --> |
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| 60 | </param> |
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| 61 | <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> |
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| 62 | <param name="out_format" type="select" label="Output format"> |
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| 63 | <option value="-outfmt 6" selected="True">Tabular</option> |
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| 64 | <option value="-outfmt 5">BLAST XML</option> |
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| 65 | <option value="-outfmt 0">Pairwise text</option> |
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| 66 | <option value="-outfmt 0 -html">Pairwise HTML</option> |
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| 67 | <option value="-outfmt 2">Query-anchored text</option> |
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| 68 | <option value="-outfmt 2 -html">Query-anchored HTML</option> |
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| 69 | <option value="-outfmt 4">Flat query-anchored text</option> |
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| 70 | <option value="-outfmt 4 -html">Flat query-anchored HTML</option> |
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| 71 | <!-- |
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| 72 | <option value="-outfmt 11">BLAST archive format (ASN.1)</option> |
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| 73 | --> |
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| 74 | </param> |
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| 75 | <conditional name="adv_opts"> |
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| 76 | <param name="adv_opts_selector" type="select" label="Advanced Options"> |
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| 77 | <option value="basic" selected="True">Hide Advanced Options</option> |
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| 78 | <option value="advanced">Show Advanced Options</option> |
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| 79 | </param> |
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| 80 | <when value="basic"> |
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| 81 | <param name="filter_query" type="hidden" value="" /> |
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| 82 | <param name="strand" type="hidden" value="" /> |
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| 83 | <param name="max_hits" type="hidden" value="" /> |
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| 84 | <param name="word_size" type="hidden" value="" /> |
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| 85 | <param name="ungapped" type="hidden" value="" /> |
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| 86 | </when> |
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| 87 | <when value="advanced"> |
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| 88 | <!-- Could use a select (yes, no, other) where other allows setting 'level window linker' --> |
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| 89 | <param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" /> |
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| 90 | <param name="strand" type="select" label="Query strand(s) to search against database/subject"> |
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| 91 | <option value="-strand both">Both</option> |
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| 92 | <option value="-strand plus">Plus (forward)</option> |
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| 93 | <option value="-strand minus">Minus (reverse complement)</option> |
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| 94 | </param> |
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| 95 | <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> |
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| 96 | <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> |
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| 97 | <validator type="in_range" min="0" /> |
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| 98 | </param> |
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| 99 | <!-- I'd like word_size to be optional, with minimum 4 for blastn --> |
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| 100 | <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4."> |
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| 101 | <validator type="in_range" min="0" /> |
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| 102 | </param> |
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| 103 | <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> |
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| 104 | </when> |
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| 105 | </conditional> |
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| 106 | </inputs> |
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| 107 | <outputs> |
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| 108 | <data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}"> |
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| 109 | <change_format> |
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| 110 | <when input="out_format" value="-outfmt 0" format="txt"/> |
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| 111 | <when input="out_format" value="-outfmt 0 -html" format="html"/> |
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| 112 | <when input="out_format" value="-outfmt 2" format="txt"/> |
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| 113 | <when input="out_format" value="-outfmt 2 -html" format="html"/> |
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| 114 | <when input="out_format" value="-outfmt 4" format="txt"/> |
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| 115 | <when input="out_format" value="-outfmt 4 -html" format="html"/> |
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| 116 | <when input="out_format" value="-outfmt 5" format="blastxml"/> |
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| 117 | </change_format> |
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| 118 | </data> |
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| 119 | </outputs> |
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| 120 | <requirements> |
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| 121 | <requirement type="binary">blastn</requirement> |
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| 122 | </requirements> |
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| 123 | <tests> |
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| 124 | <test> |
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| 125 | <param name="input_query" value="megablast_wrapper_test1.fa" ftype="fasta"/> |
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| 126 | <!-- database needs to match the entry in the blastdb.loc file (first column), which includes the last update date if appropriate --> |
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| 127 | <param name="database" value="phiX" /> |
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| 128 | <param name="blast_type" value="megablast" /> |
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| 129 | <!-- |
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| 130 | <param name="word_size" value="28" /> |
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| 131 | <param name="iden_cutoff" value="99.0" /> |
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| 132 | --> |
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| 133 | <param name="evalue_cutoff" value="10.0" /> |
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| 134 | <param name="filter_query" value="yes" /> |
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| 135 | <param name="out_format" value="6" /> |
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| 136 | <output name="output1" file="megablast_wrapper_test1.out"/> |
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| 137 | </test> |
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| 138 | </tests> |
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| 139 | <help> |
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| 140 | |
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| 141 | .. class:: warningmark |
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| 142 | |
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| 143 | **Note**. Database searches may take substantial amount of time. |
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| 144 | For large input datasets it is advisable to allow overnight processing. |
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| 145 | |
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| 146 | ----- |
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| 147 | |
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| 148 | **What it does** |
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| 149 | |
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| 150 | Search a *nucleotide database* using a *nucleotide query*, |
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| 151 | using the NCBI BLAST+ blastn command line tool. |
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| 152 | Algorithms include blastn, megablast, and discontiguous megablast. |
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| 153 | |
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| 154 | ----- |
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| 155 | |
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| 156 | **Output format** |
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| 157 | |
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| 158 | Because Galaxy focuses on processing tabular data, the default output of this tool is tabular. This contains 12 columns: |
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| 159 | |
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| 160 | 1. Id of your sequence |
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| 161 | 2. GI of the database hit |
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| 162 | 3. % identity |
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| 163 | 4. Alignment length |
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| 164 | 5. # mismatches |
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| 165 | 6. # gaps |
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| 166 | 7. Start position in your sequence |
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| 167 | 8. End position in your sequence |
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| 168 | 9. Start position in database hit |
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| 169 | 10. End position in database hit |
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| 170 | 11. E-value |
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| 171 | 12. Bit score |
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| 172 | |
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| 173 | The second option is BLAST XML output, which is designed to be parsed by another program, and is understood by other Galaxy tools. |
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| 174 | |
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| 175 | You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). |
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| 176 | The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. |
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| 177 | The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. |
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| 178 | The two query anchored outputs show a multiple sequence alignment between the query and all the matches, |
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| 179 | and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). |
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| 180 | |
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| 181 | ------- |
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| 182 | |
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| 183 | **References** |
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| 184 | |
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| 185 | Zhang et al. A Greedy Algorithm for Aligning DNA Sequences. 2000. JCB: 203-214. |
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| 186 | |
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| 187 | </help> |
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| 188 | </tool> |
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