Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @ 5:393a7a35383c draft
Uploaded v0.0.14 adding local BLAST database support.
This *requires* the matching update to the blast_datatypes repository. This adds basic wrappers for makeblastdb and blastdbinfo.
This update includes work by Edward Kirton.
author | peterjc |
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date | Fri, 09 Nov 2012 06:53:55 -0500 |
parents | 9d5beacae92b |
children | a23b0627623c |
rev | line source |
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5
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1 <tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.14"> |
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2 <description>Search protein database with protein query sequence(s)</description> |
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3 <!-- If job splitting is enabled, break up the query file into parts --> |
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4 <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject,histdb" merge_outputs="output1"></parallelism> |
3
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5 <version_command>blastp -version</version_command> |
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6 <command> |
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7 ## The command is a Cheetah template which allows some Python based syntax. |
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8 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces |
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9 blastp |
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10 -query "$query" |
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11 #if $db_opts.db_opts_selector == "db": |
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12 -db "${db_opts.database.fields.path}" |
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13 #elif $db_opts.db_opts_selector == "histdb": |
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14 -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}" |
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15 #else: |
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16 -subject "$db_opts.subject" |
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17 #end if |
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18 -task $blast_type |
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19 -evalue $evalue_cutoff |
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20 -out $output1 |
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21 ##Set the extended list here so if/when we add things, saved workflows are not affected |
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22 #if str($out_format)=="ext": |
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23 -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" |
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24 #else: |
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25 -outfmt $out_format |
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26 #end if |
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27 -num_threads 8 |
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28 #if $adv_opts.adv_opts_selector=="advanced": |
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29 $adv_opts.filter_query |
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30 -matrix $adv_opts.matrix |
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31 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string |
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32 ## Note -max_target_seqs overrides -num_descriptions and -num_alignments |
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33 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): |
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34 -max_target_seqs $adv_opts.max_hits |
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35 #end if |
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36 #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): |
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37 -word_size $adv_opts.word_size |
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38 #end if |
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39 ##Ungapped disabled for now - see comments below |
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40 ##$adv_opts.ungapped |
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41 $adv_opts.parse_deflines |
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42 ## End of advanced options: |
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43 #end if |
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44 </command> |
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45 <stdio> |
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46 <!-- Anything other than zero is an error --> |
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47 <exit_code range="1:" /> |
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48 <exit_code range=":-1" /> |
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49 <!-- In case the return code has not been set propery check stderr too --> |
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50 <regex match="Error:" /> |
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51 <regex match="EXception:" /> |
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52 </stdio> |
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53 <inputs> |
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54 <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> |
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55 <conditional name="db_opts"> |
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56 <param name="db_opts_selector" type="select" label="Subject database/sequences"> |
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57 <option value="db" selected="True">BLAST Database</option> |
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58 <option value="histdb">BLAST database from your history</option> |
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59 <option value="file">FASTA file from your history (pairwise e-values)</option> |
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60 </param> |
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61 <when value="db"> |
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62 <param name="database" type="select" label="Protein BLAST database"> |
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63 <options from_file="blastdb_p.loc"> |
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64 <column name="value" index="0"/> |
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65 <column name="name" index="1"/> |
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66 <column name="path" index="2"/> |
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67 </options> |
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68 </param> |
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69 <param name="histdb" type="hidden" value="" /> |
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70 <param name="subject" type="hidden" value="" /> |
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71 </when> |
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72 <when value="histdb"> |
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73 <param name="database" type="hidden" value="" /> |
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74 <param name="histdb" type="data" format="blastdbp" label="Protein BLAST database" /> |
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75 <param name="subject" type="hidden" value="" /> |
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76 </when> |
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77 <when value="file"> |
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78 <param name="database" type="hidden" value="" /> |
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79 <param name="histdb" type="hidden" value="" /> |
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80 <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> |
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81 </when> |
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82 </conditional> |
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83 <param name="blast_type" type="select" display="radio" label="Type of BLAST"> |
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84 <option value="blastp">blastp</option> |
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85 <option value="blastp-short">blastp-short</option> |
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86 </param> |
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87 <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> |
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88 <param name="out_format" type="select" label="Output format"> |
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89 <option value="6" selected="True">Tabular (standard 12 columns)</option> |
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90 <option value="ext">Tabular (extended 24 columns)</option> |
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91 <option value="5">BLAST XML</option> |
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92 <option value="0">Pairwise text</option> |
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93 <option value="0 -html">Pairwise HTML</option> |
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94 <option value="2">Query-anchored text</option> |
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95 <option value="2 -html">Query-anchored HTML</option> |
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96 <option value="4">Flat query-anchored text</option> |
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97 <option value="4 -html">Flat query-anchored HTML</option> |
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98 <!-- |
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99 <option value="-outfmt 11">BLAST archive format (ASN.1)</option> |
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100 --> |
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101 </param> |
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102 <conditional name="adv_opts"> |
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103 <param name="adv_opts_selector" type="select" label="Advanced Options"> |
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104 <option value="basic" selected="True">Hide Advanced Options</option> |
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105 <option value="advanced">Show Advanced Options</option> |
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106 </param> |
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107 <when value="basic" /> |
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108 <when value="advanced"> |
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109 <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> |
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110 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" /> |
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111 <param name="matrix" type="select" label="Scoring matrix"> |
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112 <option value="BLOSUM90">BLOSUM90</option> |
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113 <option value="BLOSUM80">BLOSUM80</option> |
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114 <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option> |
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115 <option value="BLOSUM50">BLOSUM50</option> |
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116 <option value="BLOSUM45">BLOSUM45</option> |
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117 <option value="PAM250">PAM250</option> |
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118 <option value="PAM70">PAM70</option> |
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119 <option value="PAM30">PAM30</option> |
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120 </param> |
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121 <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> |
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122 <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> |
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123 <validator type="in_range" min="0" /> |
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124 </param> |
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125 <!-- I'd like word_size to be optional, with minimum 2 for blastp --> |
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126 <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."> |
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127 <validator type="in_range" min="0" /> |
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128 </param> |
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129 <!-- |
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130 Can't use '-ungapped' on its own, error back is: |
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131 Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search |
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132 Tried using '-ungapped -comp_based_stats F' and blastp crashed with 'Attempt to access NULL pointer.' |
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133 <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" /> |
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134 --> |
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135 <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/> |
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136 </when> |
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137 </conditional> |
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138 </inputs> |
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139 <outputs> |
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140 <data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}"> |
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141 <change_format> |
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142 <when input="out_format" value="0" format="txt"/> |
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143 <when input="out_format" value="0 -html" format="html"/> |
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144 <when input="out_format" value="2" format="txt"/> |
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145 <when input="out_format" value="2 -html" format="html"/> |
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146 <when input="out_format" value="4" format="txt"/> |
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147 <when input="out_format" value="4 -html" format="html"/> |
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148 <when input="out_format" value="5" format="blastxml"/> |
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149 </change_format> |
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150 </data> |
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151 </outputs> |
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152 <requirements> |
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153 <requirement type="binary">blastp</requirement> |
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154 </requirements> |
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155 <tests> |
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156 <test> |
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157 <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> |
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158 <param name="db_opts_selector" value="file" /> |
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159 <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" /> |
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160 <param name="database" value="" /> |
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161 <param name="evalue_cutoff" value="1e-8" /> |
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162 <param name="blast_type" value="blastp" /> |
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163 <param name="out_format" value="5" /> |
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164 <param name="adv_opts_selector" value="advanced" /> |
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165 <param name="filter_query" value="False" /> |
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166 <param name="matrix" value="BLOSUM62" /> |
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167 <param name="max_hits" value="0" /> |
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168 <param name="word_size" value="0" /> |
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169 <param name="parse_deflines" value="True" /> |
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170 <output name="output1" file="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" /> |
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171 </test> |
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172 <test> |
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173 <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> |
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174 <param name="db_opts_selector" value="file" /> |
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175 <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" /> |
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176 <param name="database" value="" /> |
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177 <param name="evalue_cutoff" value="1e-8" /> |
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178 <param name="blast_type" value="blastp" /> |
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179 <param name="out_format" value="6" /> |
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180 <param name="adv_opts_selector" value="advanced" /> |
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181 <param name="filter_query" value="False" /> |
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182 <param name="matrix" value="BLOSUM62" /> |
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183 <param name="max_hits" value="0" /> |
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184 <param name="word_size" value="0" /> |
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185 <param name="parse_deflines" value="True" /> |
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186 <output name="output1" file="blastp_four_human_vs_rhodopsin.tabular" ftype="tabular" /> |
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187 </test> |
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188 <test> |
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189 <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> |
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190 <param name="db_opts_selector" value="file" /> |
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191 <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" /> |
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192 <param name="database" value="" /> |
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193 <param name="evalue_cutoff" value="1e-8" /> |
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194 <param name="blast_type" value="blastp" /> |
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195 <param name="out_format" value="ext" /> |
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196 <param name="adv_opts_selector" value="advanced" /> |
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197 <param name="filter_query" value="False" /> |
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198 <param name="matrix" value="BLOSUM62" /> |
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199 <param name="max_hits" value="0" /> |
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200 <param name="word_size" value="0" /> |
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201 <param name="parse_deflines" value="True" /> |
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202 <output name="output1" file="blastp_four_human_vs_rhodopsin_ext.tabular" ftype="tabular" /> |
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203 </test> |
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204 <test> |
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205 <param name="query" value="rhodopsin_proteins.fasta" ftype="fasta" /> |
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206 <param name="db_opts_selector" value="file" /> |
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207 <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> |
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208 <param name="database" value="" /> |
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209 <param name="evalue_cutoff" value="1e-8" /> |
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210 <param name="blast_type" value="blastp" /> |
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211 <param name="out_format" value="6" /> |
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212 <param name="adv_opts_selector" value="basic" /> |
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213 <output name="output1" file="blastp_rhodopsin_vs_four_human.tabular" ftype="tabular" /> |
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214 </test> |
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215 </tests> |
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216 <help> |
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217 |
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218 .. class:: warningmark |
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219 |
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220 **Note**. Database searches may take a substantial amount of time. |
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221 For large input datasets it is advisable to allow overnight processing. |
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222 |
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223 ----- |
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224 |
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225 **What it does** |
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226 |
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227 Search a *protein database* using a *protein query*, |
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228 using the NCBI BLAST+ blastp command line tool. |
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229 |
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230 ----- |
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231 |
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232 **Output format** |
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233 |
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234 Because Galaxy focuses on processing tabular data, the default output of this |
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235 tool is tabular. The standard BLAST+ tabular output contains 12 columns: |
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236 |
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237 ====== ========= ============================================ |
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238 Column NCBI name Description |
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239 ------ --------- -------------------------------------------- |
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240 1 qseqid Query Seq-id (ID of your sequence) |
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241 2 sseqid Subject Seq-id (ID of the database hit) |
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242 3 pident Percentage of identical matches |
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243 4 length Alignment length |
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244 5 mismatch Number of mismatches |
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245 6 gapopen Number of gap openings |
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246 7 qstart Start of alignment in query |
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247 8 qend End of alignment in query |
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248 9 sstart Start of alignment in subject (database hit) |
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249 10 send End of alignment in subject (database hit) |
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250 11 evalue Expectation value (E-value) |
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251 12 bitscore Bit score |
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252 ====== ========= ============================================ |
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253 |
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254 The BLAST+ tools can optionally output additional columns of information, |
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255 but this takes longer to calculate. Most (but not all) of these columns are |
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256 included by selecting the extended tabular output. The extra columns are |
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257 included *after* the standard 12 columns. This is so that you can write |
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258 workflow filtering steps that accept either the 12 or 24 column tabular |
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259 BLAST output. |
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260 |
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261 ====== ============= =========================================== |
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262 Column NCBI name Description |
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263 ------ ------------- ------------------------------------------- |
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264 13 sallseqid All subject Seq-id(s), separated by a ';' |
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265 14 score Raw score |
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266 15 nident Number of identical matches |
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267 16 positive Number of positive-scoring matches |
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268 17 gaps Total number of gaps |
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269 18 ppos Percentage of positive-scoring matches |
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270 19 qframe Query frame |
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271 20 sframe Subject frame |
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272 21 qseq Aligned part of query sequence |
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273 22 sseq Aligned part of subject sequence |
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274 23 qlen Query sequence length |
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275 24 slen Subject sequence length |
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276 ====== ============= =========================================== |
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277 |
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278 The third option is BLAST XML output, which is designed to be parsed by |
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279 another program, and is understood by some Galaxy tools. |
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280 |
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281 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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282 The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. |
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283 The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. |
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284 The two query anchored outputs show a multiple sequence alignment between the query and all the matches, |
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285 and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). |
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286 |
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287 ------- |
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288 |
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289 **References** |
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290 |
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291 Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402. |
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292 |
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293 Schaffer et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. 2001. Nucleic Acids Res. 29:2994-3005. |
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294 |
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295 </help> |
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296 </tool> |