Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_makeblastdb.xml @ 15:c16c30e9ad5b draft
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
author | peterjc |
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date | Sun, 05 Jul 2015 10:37:27 -0400 |
parents | 2fe07f50a41e |
children | b5f1f599d1fb |
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1 <tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.1.03"> |
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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 interpreter="python">check_no_duplicates.py |
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9 ##First check for duplicates (since BLAST+ 2.2.28 fails to do so) |
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10 ##and abort (via the ampersand ampersand trick) if any are found. |
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11 #for i in $input_file#"${i}" #end for# |
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12 && |
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13 makeblastdb -out "${os.path.join($outfile.files_path,'blastdb')}" |
5 | 14 $parse_seqids |
15 $hash_index | |
16 ## Single call to -in with multiple filenames space separated with outer quotes | |
17 ## (presumably any filenames with spaces would be a problem). Note this gives | |
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18 ## some extra spaces, e.g. -in "file1 file2 file3 " but BLAST seems happy: |
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19 -in "#for i in $input_file#${i} #end for#" |
5 | 20 #if $title: |
21 -title "$title" | |
22 #else: | |
23 ##Would default to being based on the cryptic Galaxy filenames, which is unhelpful | |
24 -title "BLAST Database" | |
25 #end if | |
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26 -dbtype $dbtype |
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27 ## -------------------------------------------------------------------- |
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28 ## Masking |
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29 ## -------------------------------------------------------------------- |
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30 ## HACK: If no mask files, evaluates as a list with just None in it: |
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31 ## See Trello issue https://trello.com/c/lp5YmA1O |
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32 #if ' '.join( map(str, $mask_data_file) ) != 'None': |
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33 #for i in $mask_data_file: |
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34 -mask_data "${i}" |
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35 #end for |
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36 #end if |
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37 ## -------------------------------------------------------------------- |
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38 ## Taxonomy |
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39 ## -------------------------------------------------------------------- |
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40 #if $tax.taxselect == 'id': |
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41 -taxid $tax.taxid |
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42 ## TODO - Can we use a tabular file for the taxonomy mapping? |
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43 ## #else if $tax.taxselect == 'map': |
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44 ## -taxid_map $tax.taxmap |
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45 #end if |
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46 ## -------------------------------------------------------------------- |
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47 ## Capture the stdout log information to the primary file (plain text): |
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48 > "$outfile" |
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49 </command> |
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50 <inputs> |
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51 <param name="dbtype" type="select" display="radio" label="Molecule type of input"> |
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52 <option value="prot">protein</option> |
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53 <option value="nucl">nucleotide</option> |
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54 </param> |
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55 <!-- TODO Allow merging of existing BLAST databases (conditional on the database type)? |
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56 NOTE Double check the new database would be self contained first |
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57 --> |
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58 <!-- Note this is a mandatory parameter - default should be most recent FASTA file --> |
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59 <param name="input_file" type="data" multiple="true" optional="false" format="fasta" label="Input FASTA files(s)" help="One or more FASTA files" /> |
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60 <param name="title" type="text" value="" label="Title for BLAST database" help="This is the database name shown in BLAST search output" /> |
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61 <param name="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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62 <param name="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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63 <!-- SEQUENCE MASKING OPTIONS --> |
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64 <!-- Note this is an optional parameter - default should be NO files --> |
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65 <param name="mask_data_file" 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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66 <!-- TODO - Option to create GI indexed masking data? via -gi_mask and -gi_mask_name? --> |
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67 <!-- TAXONOMY OPTIONS --> |
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68 <conditional name="tax"> |
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69 <param name="taxselect" type="select" label="Taxonomy options"> |
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70 <option value="">Do not assign a Taxonomy ID to the sequences</option> |
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71 <option value="id">Assign the same Taxonomy ID to all the sequences</option> |
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72 <!-- |
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73 <option value="map">Supply text file mapping sequence IDs to taxnomy IDs</option> |
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74 --> |
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75 </param> |
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76 <when value=""> |
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77 </when> |
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78 <when value="id"> |
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79 <param name="taxid" type="integer" value="" label="NCBI taxonomy ID" help="Integer >=0, e.g. 9606 for Homo sapiens" min="0" /> |
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80 </when> |
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81 <!-- TODO: File format? |
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82 <when value="map"> |
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83 <param name="taxmap" type="data" format="txt" label="Seq ID : Tax ID mapping file" help="Format: SequenceId TaxonomyId" /> |
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84 </when> |
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85 --> |
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86 </conditional> |
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87 </inputs> |
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88 <outputs> |
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89 <!-- If we only accepted one FASTA file, we could use its human name here... --> |
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90 <data name="outfile" format="data" label="${dbtype.value_label} BLAST database from ${on_string}"> |
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91 <change_format> |
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92 <when input="dbtype" value="nucl" format="blastdbn" /> |
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93 <when input="dbtype" value="prot" format="blastdbp" /> |
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94 </change_format> |
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95 </data> |
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96 </outputs> |
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97 <tests> |
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98 <!-- Note the (two line) PIN file is not reproducible run to run. |
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99 The same applies to the NIN file for nucleotide database. |
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100 Likewise there is a datestamp in the log file as well, so use contains comparison |
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101 With and without the masking makes no difference. |
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102 With and without the taxid the only real difference is in the *.phr file. |
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103 --> |
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104 <test> |
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105 <param name="dbtype" value="prot" /> |
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106 <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> |
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107 <param name="title" value="Just 4 human proteins" /> |
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108 <param name="parse_seqids" value="" /> |
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109 <param name="hash_index" value="true" /> |
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110 <output name="out_file" compare="contains" file="four_human_proteins.fasta.log.txt" ftype="blastdbp"> |
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111 <extra_files type="file" value="four_human_proteins.fasta.phr" name="blastdb.phr" /> |
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112 <extra_files type="file" value="four_human_proteins.fasta.pin" name="blastdb.pin" lines_diff="2" /> |
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113 <extra_files type="file" value="four_human_proteins.fasta.psq" name="blastdb.psq" /> |
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114 <extra_files type="file" value="four_human_proteins.fasta.pog" name="blastdb.pog" /> |
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115 <extra_files type="file" value="four_human_proteins.fasta.phd" name="blastdb.phd" /> |
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116 <extra_files type="file" value="four_human_proteins.fasta.phi" name="blastdb.phi" /> |
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117 <extra_files type="file" value="four_human_proteins.fasta.psd" name="blastdb.psd" /> |
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118 <extra_files type="file" value="four_human_proteins.fasta.psi" name="blastdb.psi" /> |
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119 </output> |
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120 </test> |
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121 <test> |
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122 <param name="dbtype" value="prot" /> |
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123 <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> |
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124 <param name="title" value="Just 4 human proteins" /> |
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125 <param name="parse_seqids" value="" /> |
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126 <param name="hash_index" value="true" /> |
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127 <param name="taxselect" value="id" /> |
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128 <param name="taxid" value="9606" /> |
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129 <output name="out_file" compare="contains" file="four_human_proteins_taxid.fasta.log.txt" ftype="blastdbp"> |
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130 <extra_files type="file" value="four_human_proteins_taxid.fasta.phr" name="blastdb.phr" /> |
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131 <extra_files type="file" value="four_human_proteins_taxid.fasta.pin" name="blastdb.pin" lines_diff="2" /> |
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132 <extra_files type="file" value="four_human_proteins_taxid.fasta.psq" name="blastdb.psq" /> |
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133 <extra_files type="file" value="four_human_proteins_taxid.fasta.pog" name="blastdb.pog" /> |
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134 <extra_files type="file" value="four_human_proteins_taxid.fasta.phd" name="blastdb.phd" /> |
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135 <extra_files type="file" value="four_human_proteins_taxid.fasta.phi" name="blastdb.phi" /> |
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136 <extra_files type="file" value="four_human_proteins_taxid.fasta.psd" name="blastdb.psd" /> |
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137 <extra_files type="file" value="four_human_proteins_taxid.fasta.psi" name="blastdb.psi" /> |
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138 </output> |
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139 </test> |
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140 <test> |
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141 <param name="dbtype" value="prot" /> |
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142 <param name="input_file" value="four_human_proteins.fasta" ftype="fasta" /> |
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143 <param name="title" value="Just 4 human proteins" /> |
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144 <param name="parse_seqids" value="" /> |
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145 <param name="hash_index" value="true" /> |
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146 <param name="mask_data_file" value="segmasker_four_human.maskinfo-asn1" ftype="maskinfo-asn1" /> |
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147 <output name="out_file" compare="contains" file="four_human_proteins.fasta.log.txt" ftype="blastdbp"> |
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148 <extra_files type="file" value="four_human_proteins.fasta.phr" name="blastdb.phr" /> |
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149 <extra_files type="file" value="four_human_proteins.fasta.pin" name="blastdb.pin" lines_diff="2" /> |
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150 <extra_files type="file" value="four_human_proteins.fasta.psq" name="blastdb.psq" /> |
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151 <extra_files type="file" value="four_human_proteins.fasta.pog" name="blastdb.pog" /> |
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152 <extra_files type="file" value="four_human_proteins.fasta.phd" name="blastdb.phd" /> |
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153 <extra_files type="file" value="four_human_proteins.fasta.phi" name="blastdb.phi" /> |
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154 <extra_files type="file" value="four_human_proteins.fasta.psd" name="blastdb.psd" /> |
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155 <extra_files type="file" value="four_human_proteins.fasta.psi" name="blastdb.psi" /> |
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156 </output> |
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157 </test> |
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158 <test> |
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159 <param name="dbtype" value="nucl" /> |
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160 <param name="input_file" value="three_human_mRNA.fasta" ftype="fasta" /> |
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161 <param name="title" value="Just 3 human mRNA sequences" /> |
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162 <param name="parse_seqids" value="" /> |
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163 <param name="hash_index" value="true" /> |
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164 <param name="taxselect" value="id" /> |
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165 <param name="taxid" value="9606" /> |
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166 <output name="out_file" compare="contains" file="three_human_mRNA.fasta.log.txt" ftype="blastdbn"> |
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167 <extra_files type="file" value="three_human_mRNA.fasta.nhr" name="blastdb.nhr" /> |
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168 <extra_files type="file" value="three_human_mRNA.fasta.nin" name="blastdb.nin" lines_diff="2" /> |
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169 <extra_files type="file" value="three_human_mRNA.fasta.nsq" name="blastdb.nsq" /> |
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170 <extra_files type="file" value="three_human_mRNA.fasta.nog" name="blastdb.nog" /> |
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171 <extra_files type="file" value="three_human_mRNA.fasta.nhd" name="blastdb.nhd" /> |
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172 <extra_files type="file" value="three_human_mRNA.fasta.nhi" name="blastdb.nhi" /> |
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173 <extra_files type="file" value="three_human_mRNA.fasta.nsd" name="blastdb.nsd" /> |
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174 <extra_files type="file" value="three_human_mRNA.fasta.nsi" name="blastdb.nsi" /> |
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175 </output> |
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176 </test> |
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177 </tests> |
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178 <help> |
5 | 179 **What it does** |
180 | |
181 Make BLAST database from one or more FASTA files and/or BLAST databases. | |
182 | |
183 This is a wrapper for the NCBI BLAST+ tool 'makeblastdb', which is the | |
184 replacement for the 'formatdb' tool in the NCBI 'legacy' BLAST suite. | |
185 | |
186 <!-- | |
187 Applying masks to an existing BLAST database will not change the original database; a new database will be created. | |
188 For this reason, it's best to apply all masks at once to minimize the number of unnecessary intermediate databases. | |
189 --> | |
190 | |
191 **Documentation** | |
192 | |
193 http://www.ncbi.nlm.nih.gov/books/NBK1763/ | |
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194 |
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195 **References** |
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196 |
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 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.
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198 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.
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199 |
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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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200 @REFERENCES@ |
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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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201 </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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202 <expand macro="blast_citations" /> |
5 | 203 </tool> |