Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_makeblastdb.xml @ 31:0e3cf9594bb7 draft
Update with window size fix
author | peterjc |
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date | Tue, 07 Jun 2022 12:15:44 +0000 |
parents | 5edc472ec434 |
children | a52d2d93e595 |
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"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
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1 <tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
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2 <description>Make BLAST database</description> |
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3 <macros> |
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4 <token name="@BINARY@">makeblastdb</token> |
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5 <import>ncbi_macros.xml</import> |
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6 </macros> |
31 | 7 <expand macro="preamble"> |
8 <requirement type="package" version="3.9">python</requirement> | |
9 </expand> | |
23 | 10 <command detect_errors="aggressive" strict="true"><![CDATA[ |
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11 python $__tool_directory__/check_no_duplicates.py |
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12 ##First check for duplicates (since BLAST+ 2.2.28 fails to do so) |
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13 ##and abort (via the ampersand ampersand trick) if any are found. |
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14 #for i in $input_file#'${i}' #end for# |
23 | 15 && |
16 ##makeblastdb does not like input redirects of the sort | |
17 ##makeblastdb -in <(gunzip -c gzipped_fasta_file) | |
18 ##therefore we're cramming everything | |
19 ##into a single cat command below | |
20 cat | |
21 #for i in $input_file: | |
25 | 22 #if $i.is_of_type('fasta.gz') and $i.ext != "fasta": |
23 | 23 <(gunzip -c ${i}) |
24 #else: | |
25 ${i} | |
26 #end if | |
27 #end for | |
28 | makeblastdb -out '${os.path.join($outfile.files_path, "blastdb")}' | |
29 | 29 -blastdb_version 4 |
5 | 30 $parse_seqids |
31 $hash_index | |
23 | 32 -in - |
5 | 33 #if $title: |
23 | 34 -title '${title}' |
5 | 35 #else: |
36 ##Would default to being based on the cryptic Galaxy filenames, which is unhelpful | |
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37 -title 'BLAST Database' |
5 | 38 #end if |
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39 -dbtype $dbtype |
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40 ## -------------------------------------------------------------------- |
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41 ## Masking |
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42 ## -------------------------------------------------------------------- |
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43 ## HACK: If no mask files, evaluates as a list with just None in it: |
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44 ## See Trello issue https://trello.com/c/lp5YmA1O |
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45 #if ' '.join( map(str, $mask_data_file) ) != 'None': |
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46 #for i in $mask_data_file: |
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47 -mask_data '${i}' |
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48 #end for |
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49 #end if |
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50 ## -------------------------------------------------------------------- |
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51 ## Taxonomy |
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52 ## -------------------------------------------------------------------- |
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53 #if $tax.taxselect == 'id': |
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54 -taxid $tax.taxid |
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55 ## TODO - Can we use a tabular file for the taxonomy mapping? |
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56 ## #else if $tax.taxselect == 'map': |
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57 ## -taxid_map $tax.taxmap |
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58 #end if |
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59 ## -------------------------------------------------------------------- |
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60 ## Capture the stdout log information to the primary file (plain text): |
23 | 61 > '$outfile' |
62 ]]></command> | |
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63 <inputs> |
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64 <param argument="-dbtype" type="select" display="radio" label="Molecule type of input"> |
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65 <option value="prot">protein</option> |
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66 <option value="nucl">nucleotide</option> |
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67 </param> |
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68 <!-- TODO Allow merging of existing BLAST databases (conditional on the database type)? |
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69 NOTE Double check the new database would be self contained first |
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70 --> |
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71 <!-- Note this is a mandatory parameter - default should be most recent FASTA file --> |
23 | 72 <param name="input_file" argument="-in" type="data" multiple="true" optional="false" format="fasta,fasta.gz" label="Input FASTA files(s)" help="One or more FASTA files" /> |
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73 <param argument="-title" type="text" value="" label="Title for BLAST database" help="This is the database name shown in BLAST search output" /> |
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74 <param argument="-parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="false" label="Parse the sequence identifiers" help="This is only advised if your FASTA file follows the NCBI naming conventions using pipe '|' symbols" /> |
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75 <param argument="-hash_index" type="boolean" truevalue="-hash_index" falsevalue="" checked="true" label="Enable the creation of sequence hash values" help="These hash values can then be used to quickly determine if a given sequence data exists in this BLAST database." /> |
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76 <!-- SEQUENCE MASKING OPTIONS --> |
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77 <!-- Note this is an optional parameter - default should be NO files --> |
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78 <param name="mask_data_file" argument="-mask_data" type="data" multiple="true" optional="true" value="" format="maskinfo-asn1,maskinfo-asn1-binary" label="Optional ASN.1 file(s) containing masking data" help="As produced by NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)" /> |
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79 <!-- TODO - Option to create GI indexed masking data? via -gi_mask and -gi_mask_name? --> |
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80 <!-- TAXONOMY OPTIONS --> |
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81 <conditional name="tax"> |
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82 <param name="taxselect" type="select" label="Taxonomy options"> |
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83 <option value="">Do not assign a Taxonomy ID to the sequences</option> |
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84 <option value="id">Assign the same Taxonomy ID to all the sequences</option> |
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85 <!-- |
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86 <option value="map">Supply text file mapping sequence IDs to taxnomy IDs</option> |
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87 --> |
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88 </param> |
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89 <when value=""> |
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90 </when> |
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91 <when value="id"> |
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92 <param argument="-taxid" type="integer" min="0" value="" label="NCBI taxonomy ID" help="Integer >=0, e.g. 9606 for Homo sapiens" /> |
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93 </when> |
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94 <!-- TODO: File format? |
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95 <when value="map"> |
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96 <param name="taxmap" argument="-taxid_map" type="data" format="txt" label="Seq ID : Tax ID mapping file" help="Format: SequenceId TaxonomyId" /> |
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97 </when> |
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98 --> |
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99 </conditional> |
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100 </inputs> |
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101 <outputs> |
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102 <!-- If we only accepted one FASTA file, we could use its human name here... --> |
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103 <data name="outfile" format="data" label="${dbtype.value_label} BLAST database from ${on_string}"> |
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104 <change_format> |
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105 <when input="dbtype" value="nucl" format="blastdbn" /> |
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106 <when input="dbtype" value="prot" format="blastdbp" /> |
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107 </change_format> |
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108 </data> |
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109 </outputs> |
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110 <tests> |
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111 <!-- Note the (two line) PIN file is not reproducible run to run. |
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112 The same applies to the NIN file for nucleotide database. |
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113 Likewise there is a datestamp in the log file as well, so use contains comparison |
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114 With and without the masking makes no difference. |
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115 With and without the taxid the only real difference is in the *.phr file. |
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116 --> |
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117 <test> |
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118 <param name="dbtype" value="prot" /> |
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119 <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> |
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120 <param name="title" value="Just 4 human proteins" /> |
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121 <param name="parse_seqids" value="" /> |
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122 <param name="hash_index" value="true" /> |
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123 <output name="outfile" compare="contains" file="four_human_proteins.fasta.log.txt" ftype="blastdbp"> |
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124 <extra_files type="file" value="four_human_proteins.fasta.phr" name="blastdb.phr" /> |
23 | 125 <extra_files type="file" value="four_human_proteins.fasta.pin" name="blastdb.pin" compare="sim_size" delta="0" /> |
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126 <extra_files type="file" value="four_human_proteins.fasta.psq" name="blastdb.psq" /> |
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127 <extra_files type="file" value="four_human_proteins.fasta.pog" name="blastdb.pog" /> |
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128 <extra_files type="file" value="four_human_proteins.fasta.phd" name="blastdb.phd" /> |
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129 <extra_files type="file" value="four_human_proteins.fasta.phi" name="blastdb.phi" /> |
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130 <extra_files type="file" value="four_human_proteins.fasta.psd" name="blastdb.psd" /> |
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131 <extra_files type="file" value="four_human_proteins.fasta.psi" name="blastdb.psi" /> |
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132 </output> |
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133 </test> |
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134 <test> |
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135 <param name="dbtype" value="prot" /> |
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136 <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> |
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137 <param name="title" value="Just 4 human proteins" /> |
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138 <param name="parse_seqids" value="" /> |
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139 <param name="hash_index" value="true" /> |
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140 <param name="taxselect" value="id" /> |
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141 <param name="taxid" value="9606" /> |
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142 <output name="outfile" compare="contains" file="four_human_proteins_taxid.fasta.log.txt" ftype="blastdbp"> |
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143 <extra_files type="file" value="four_human_proteins_taxid.fasta.phr" name="blastdb.phr" /> |
23 | 144 <extra_files type="file" value="four_human_proteins_taxid.fasta.pin" name="blastdb.pin" compare="sim_size" delta="0" /> |
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145 <extra_files type="file" value="four_human_proteins_taxid.fasta.psq" name="blastdb.psq" /> |
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146 <extra_files type="file" value="four_human_proteins_taxid.fasta.pog" name="blastdb.pog" /> |
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147 <extra_files type="file" value="four_human_proteins_taxid.fasta.phd" name="blastdb.phd" /> |
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148 <extra_files type="file" value="four_human_proteins_taxid.fasta.phi" name="blastdb.phi" /> |
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149 <extra_files type="file" value="four_human_proteins_taxid.fasta.psd" name="blastdb.psd" /> |
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150 <extra_files type="file" value="four_human_proteins_taxid.fasta.psi" name="blastdb.psi" /> |
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151 </output> |
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152 </test> |
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153 <test> |
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154 <param name="dbtype" value="prot" /> |
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155 <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> |
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156 <param name="title" value="Just 4 human proteins" /> |
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157 <param name="parse_seqids" value="" /> |
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158 <param name="hash_index" value="true" /> |
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159 <param name="mask_data_file" value="segmasker_four_human.maskinfo-asn1" ftype="maskinfo-asn1" /> |
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160 <output name="outfile" compare="contains" file="four_human_proteins.fasta.log.txt" ftype="blastdbp"> |
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161 <extra_files type="file" value="four_human_proteins.fasta.phr" name="blastdb.phr" /> |
23 | 162 <extra_files type="file" value="four_human_proteins.fasta.pin" name="blastdb.pin" compare="sim_size" delta="0" /> |
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163 <extra_files type="file" value="four_human_proteins.fasta.psq" name="blastdb.psq" /> |
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164 <extra_files type="file" value="four_human_proteins.fasta.pog" name="blastdb.pog" /> |
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165 <extra_files type="file" value="four_human_proteins.fasta.phd" name="blastdb.phd" /> |
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166 <extra_files type="file" value="four_human_proteins.fasta.phi" name="blastdb.phi" /> |
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167 <extra_files type="file" value="four_human_proteins.fasta.psd" name="blastdb.psd" /> |
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168 <extra_files type="file" value="four_human_proteins.fasta.psi" name="blastdb.psi" /> |
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169 </output> |
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170 </test> |
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171 <test> |
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172 <param name="dbtype" value="nucl" /> |
23 | 173 <param name="input_file" value="three_human_mRNA.fasta.gz" ftype="fasta.gz" /> |
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174 <param name="title" value="Just 3 human mRNA sequences" /> |
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175 <param name="parse_seqids" value="" /> |
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176 <param name="hash_index" value="true" /> |
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177 <param name="taxselect" value="id" /> |
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178 <param name="taxid" value="9606" /> |
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179 <output name="outfile" compare="contains" file="three_human_mRNA.fasta.log.txt" ftype="blastdbn"> |
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180 <extra_files type="file" value="three_human_mRNA.fasta.nhr" name="blastdb.nhr" /> |
23 | 181 <extra_files type="file" value="three_human_mRNA.fasta.nin" name="blastdb.nin" compare="sim_size" delta="8" /> |
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182 <extra_files type="file" value="three_human_mRNA.fasta.nsq" name="blastdb.nsq" /> |
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183 <extra_files type="file" value="three_human_mRNA.fasta.nog" name="blastdb.nog" /> |
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184 <extra_files type="file" value="three_human_mRNA.fasta.nhd" name="blastdb.nhd" /> |
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185 <extra_files type="file" value="three_human_mRNA.fasta.nhi" name="blastdb.nhi" /> |
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186 <extra_files type="file" value="three_human_mRNA.fasta.nsd" name="blastdb.nsd" /> |
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187 <extra_files type="file" value="three_human_mRNA.fasta.nsi" name="blastdb.nsi" /> |
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188 </output> |
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189 </test> |
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190 </tests> |
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191 <help> |
5 | 192 **What it does** |
193 | |
194 Make BLAST database from one or more FASTA files and/or BLAST databases. | |
195 | |
196 This is a wrapper for the NCBI BLAST+ tool 'makeblastdb', which is the | |
197 replacement for the 'formatdb' tool in the NCBI 'legacy' BLAST suite. | |
198 | |
23 | 199 More information about makeblastdb can be found in the `BLAST Command Line Applications User Manual`_. |
200 | |
201 .. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/ | |
202 | |
203 | |
5 | 204 <!-- |
205 Applying masks to an existing BLAST database will not change the original database; a new database will be created. | |
206 For this reason, it's best to apply all masks at once to minimize the number of unnecessary intermediate databases. | |
207 --> | |
208 | |
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209 **References** |
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210 |
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211 If you use this Galaxy tool in work leading to a scientific publication please |
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212 cite the following papers: |
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213 |
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214 @REFERENCES@ |
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215 </help> |
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216 <expand macro="blast_citations" /> |
5 | 217 </tool> |