Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_makeblastdb.xml @ 22:6f386c5dc4fb draft
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
author | peterjc |
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date | Mon, 18 Sep 2017 06:21:27 -0400 |
parents | 3034ce97dd33 |
children | 31e517610e1f |
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1 <tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="@WRAPPER_VERSION@"> |
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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> |
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7 <expand macro="preamble" /> |
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8 <command detect_errors="aggressive" strict="true"> |
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9 python $__tool_directory__/check_no_duplicates.py |
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10 ##First check for duplicates (since BLAST+ 2.2.28 fails to do so) |
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11 ##and abort (via the ampersand ampersand trick) if any are found. |
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12 #for i in $input_file#'${i}' #end for# |
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13 && |
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14 makeblastdb -out '${os.path.join($outfile.files_path, "blastdb")}' |
5 | 15 $parse_seqids |
16 $hash_index | |
17 ## Single call to -in with multiple filenames space separated with outer quotes | |
18 ## (presumably any filenames with spaces would be a problem). Note this gives | |
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19 ## some extra spaces, e.g. -in "file1 file2 file3 " but BLAST seems happy: |
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20 -in '#for i in $input_file#${i} #end for#' |
5 | 21 #if $title: |
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22 -title '$title' |
5 | 23 #else: |
24 ##Would default to being based on the cryptic Galaxy filenames, which is unhelpful | |
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25 -title 'BLAST Database' |
5 | 26 #end if |
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27 -dbtype $dbtype |
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28 ## -------------------------------------------------------------------- |
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29 ## Masking |
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30 ## -------------------------------------------------------------------- |
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31 ## HACK: If no mask files, evaluates as a list with just None in it: |
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32 ## See Trello issue https://trello.com/c/lp5YmA1O |
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33 #if ' '.join( map(str, $mask_data_file) ) != 'None': |
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34 #for i in $mask_data_file: |
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35 -mask_data '${i}' |
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36 #end for |
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37 #end if |
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38 ## -------------------------------------------------------------------- |
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39 ## Taxonomy |
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40 ## -------------------------------------------------------------------- |
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41 #if $tax.taxselect == 'id': |
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42 -taxid $tax.taxid |
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43 ## TODO - Can we use a tabular file for the taxonomy mapping? |
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44 ## #else if $tax.taxselect == 'map': |
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45 ## -taxid_map $tax.taxmap |
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46 #end if |
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47 ## -------------------------------------------------------------------- |
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48 ## Capture the stdout log information to the primary file (plain text): |
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49 > "$outfile" |
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50 </command> |
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51 <inputs> |
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52 <param argument="-dbtype" type="select" display="radio" label="Molecule type of input"> |
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53 <option value="prot">protein</option> |
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54 <option value="nucl">nucleotide</option> |
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55 </param> |
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56 <!-- TODO Allow merging of existing BLAST databases (conditional on the database type)? |
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57 NOTE Double check the new database would be self contained first |
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58 --> |
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59 <!-- Note this is a mandatory parameter - default should be most recent FASTA file --> |
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60 <param name="input_file" argument="-in" type="data" multiple="true" optional="false" format="fasta" label="Input FASTA files(s)" help="One or more FASTA files" /> |
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61 <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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62 <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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63 <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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64 <!-- SEQUENCE MASKING OPTIONS --> |
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65 <!-- Note this is an optional parameter - default should be NO files --> |
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66 <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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67 <!-- TODO - Option to create GI indexed masking data? via -gi_mask and -gi_mask_name? --> |
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68 <!-- TAXONOMY OPTIONS --> |
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69 <conditional name="tax"> |
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70 <param name="taxselect" type="select" label="Taxonomy options"> |
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71 <option value="">Do not assign a Taxonomy ID to the sequences</option> |
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72 <option value="id">Assign the same Taxonomy ID to all the sequences</option> |
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73 <!-- |
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74 <option value="map">Supply text file mapping sequence IDs to taxnomy IDs</option> |
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75 --> |
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76 </param> |
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77 <when value=""> |
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78 </when> |
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79 <when value="id"> |
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80 <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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81 </when> |
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82 <!-- TODO: File format? |
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83 <when value="map"> |
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84 <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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85 </when> |
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86 --> |
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87 </conditional> |
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88 </inputs> |
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89 <outputs> |
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90 <!-- If we only accepted one FASTA file, we could use its human name here... --> |
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91 <data name="outfile" format="data" label="${dbtype.value_label} BLAST database from ${on_string}"> |
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92 <change_format> |
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93 <when input="dbtype" value="nucl" format="blastdbn" /> |
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94 <when input="dbtype" value="prot" format="blastdbp" /> |
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95 </change_format> |
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96 </data> |
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97 </outputs> |
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98 <tests> |
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99 <!-- Note the (two line) PIN file is not reproducible run to run. |
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100 The same applies to the NIN file for nucleotide database. |
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101 Likewise there is a datestamp in the log file as well, so use contains comparison |
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102 With and without the masking makes no difference. |
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103 With and without the taxid the only real difference is in the *.phr file. |
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104 --> |
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105 <test> |
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106 <param name="dbtype" value="prot" /> |
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107 <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> |
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108 <param name="title" value="Just 4 human proteins" /> |
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109 <param name="parse_seqids" value="" /> |
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110 <param name="hash_index" value="true" /> |
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111 <output name="outfile" compare="contains" file="four_human_proteins.fasta.log.txt" ftype="blastdbp"> |
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112 <extra_files type="file" value="four_human_proteins.fasta.phr" name="blastdb.phr" /> |
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113 <extra_files type="file" value="four_human_proteins.fasta.pin" name="blastdb.pin" lines_diff="2" /> |
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114 <extra_files type="file" value="four_human_proteins.fasta.psq" name="blastdb.psq" /> |
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115 <extra_files type="file" value="four_human_proteins.fasta.pog" name="blastdb.pog" /> |
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116 <extra_files type="file" value="four_human_proteins.fasta.phd" name="blastdb.phd" /> |
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117 <extra_files type="file" value="four_human_proteins.fasta.phi" name="blastdb.phi" /> |
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118 <extra_files type="file" value="four_human_proteins.fasta.psd" name="blastdb.psd" /> |
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119 <extra_files type="file" value="four_human_proteins.fasta.psi" name="blastdb.psi" /> |
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120 </output> |
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121 </test> |
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122 <test> |
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123 <param name="dbtype" value="prot" /> |
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124 <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> |
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125 <param name="title" value="Just 4 human proteins" /> |
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126 <param name="parse_seqids" value="" /> |
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127 <param name="hash_index" value="true" /> |
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128 <param name="taxselect" value="id" /> |
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129 <param name="taxid" value="9606" /> |
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130 <output name="outfile" compare="contains" file="four_human_proteins_taxid.fasta.log.txt" ftype="blastdbp"> |
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131 <extra_files type="file" value="four_human_proteins_taxid.fasta.phr" name="blastdb.phr" /> |
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132 <extra_files type="file" value="four_human_proteins_taxid.fasta.pin" name="blastdb.pin" lines_diff="2" /> |
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133 <extra_files type="file" value="four_human_proteins_taxid.fasta.psq" name="blastdb.psq" /> |
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134 <extra_files type="file" value="four_human_proteins_taxid.fasta.pog" name="blastdb.pog" /> |
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135 <extra_files type="file" value="four_human_proteins_taxid.fasta.phd" name="blastdb.phd" /> |
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136 <extra_files type="file" value="four_human_proteins_taxid.fasta.phi" name="blastdb.phi" /> |
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137 <extra_files type="file" value="four_human_proteins_taxid.fasta.psd" name="blastdb.psd" /> |
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138 <extra_files type="file" value="four_human_proteins_taxid.fasta.psi" name="blastdb.psi" /> |
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139 </output> |
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140 </test> |
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141 <test> |
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142 <param name="dbtype" value="prot" /> |
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143 <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> |
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144 <param name="title" value="Just 4 human proteins" /> |
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145 <param name="parse_seqids" value="" /> |
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146 <param name="hash_index" value="true" /> |
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147 <param name="mask_data_file" value="segmasker_four_human.maskinfo-asn1" ftype="maskinfo-asn1" /> |
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148 <output name="outfile" compare="contains" file="four_human_proteins.fasta.log.txt" ftype="blastdbp"> |
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149 <extra_files type="file" value="four_human_proteins.fasta.phr" name="blastdb.phr" /> |
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150 <extra_files type="file" value="four_human_proteins.fasta.pin" name="blastdb.pin" lines_diff="2" /> |
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151 <extra_files type="file" value="four_human_proteins.fasta.psq" name="blastdb.psq" /> |
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152 <extra_files type="file" value="four_human_proteins.fasta.pog" name="blastdb.pog" /> |
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153 <extra_files type="file" value="four_human_proteins.fasta.phd" name="blastdb.phd" /> |
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154 <extra_files type="file" value="four_human_proteins.fasta.phi" name="blastdb.phi" /> |
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155 <extra_files type="file" value="four_human_proteins.fasta.psd" name="blastdb.psd" /> |
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156 <extra_files type="file" value="four_human_proteins.fasta.psi" name="blastdb.psi" /> |
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157 </output> |
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158 </test> |
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159 <test> |
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160 <param name="dbtype" value="nucl" /> |
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161 <param name="input_file" value="three_human_mRNA.fasta" ftype="fasta" /> |
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162 <param name="title" value="Just 3 human mRNA sequences" /> |
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163 <param name="parse_seqids" value="" /> |
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164 <param name="hash_index" value="true" /> |
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165 <param name="taxselect" value="id" /> |
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166 <param name="taxid" value="9606" /> |
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167 <output name="outfile" compare="contains" file="three_human_mRNA.fasta.log.txt" ftype="blastdbn"> |
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168 <extra_files type="file" value="three_human_mRNA.fasta.nhr" name="blastdb.nhr" /> |
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169 <extra_files type="file" value="three_human_mRNA.fasta.nin" name="blastdb.nin" lines_diff="2" /> |
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170 <extra_files type="file" value="three_human_mRNA.fasta.nsq" name="blastdb.nsq" /> |
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171 <extra_files type="file" value="three_human_mRNA.fasta.nog" name="blastdb.nog" /> |
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172 <extra_files type="file" value="three_human_mRNA.fasta.nhd" name="blastdb.nhd" /> |
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173 <extra_files type="file" value="three_human_mRNA.fasta.nhi" name="blastdb.nhi" /> |
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174 <extra_files type="file" value="three_human_mRNA.fasta.nsd" name="blastdb.nsd" /> |
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175 <extra_files type="file" value="three_human_mRNA.fasta.nsi" name="blastdb.nsi" /> |
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176 </output> |
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177 </test> |
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178 </tests> |
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179 <help> |
5 | 180 **What it does** |
181 | |
182 Make BLAST database from one or more FASTA files and/or BLAST databases. | |
183 | |
184 This is a wrapper for the NCBI BLAST+ tool 'makeblastdb', which is the | |
185 replacement for the 'formatdb' tool in the NCBI 'legacy' BLAST suite. | |
186 | |
187 <!-- | |
188 Applying masks to an existing BLAST database will not change the original database; a new database will be created. | |
189 For this reason, it's best to apply all masks at once to minimize the number of unnecessary intermediate databases. | |
190 --> | |
191 | |
192 **Documentation** | |
193 | |
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194 https://www.ncbi.nlm.nih.gov/books/NBK279690/ |
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195 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
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196 **References** |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
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197 |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
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198 If you use this Galaxy tool in work leading to a scientific publication please |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
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199 cite the following papers: |
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
peterjc
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200 |
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4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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201 @REFERENCES@ |
10
70e7dcbf6573
Uploaded v0.0.20, handles dependencies via package_blast_plus_2_2_26, development moved to GitHub, RST README, MIT licence, citation information, more tests, percentage identity option to BLASTN, cElementTree to ElementTree fallback.
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202 </help> |
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2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
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203 <expand macro="blast_citations" /> |
5 | 204 </tool> |