Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @ 9:9dabbfd73c8a draft
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
Also includes other minor improvements.
author | peterjc |
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date | Thu, 25 Apr 2013 09:38:37 -0400 |
parents | 1f546099212f |
children | 70e7dcbf6573 |
rev | line source |
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9
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
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1 <tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.19"> |
3
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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> |
9
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Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
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5 <requirements> |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
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6 <requirement type="binary">blastp</requirement> |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
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7 <requirement type="package" version="2.2.26+">blast+</requirement> |
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
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8 </requirements> |
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9 <version_command>blastp -version</version_command> |
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10 <command> |
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11 ## The command is a Cheetah template which allows some Python based syntax. |
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12 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces |
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13 blastp |
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14 -query "$query" |
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15 #if $db_opts.db_opts_selector == "db": |
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16 -db "${db_opts.database.fields.path}" |
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17 #elif $db_opts.db_opts_selector == "histdb": |
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18 -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}" |
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19 #else: |
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20 -subject "$db_opts.subject" |
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21 #end if |
643338ac83c0
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22 -task $blast_type |
643338ac83c0
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23 -evalue $evalue_cutoff |
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9dabbfd73c8a
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24 -out "$output1" |
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25 ##Set the extended list here so if/when we add things, saved workflows are not affected |
643338ac83c0
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26 #if str($out_format)=="ext": |
643338ac83c0
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27 -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" |
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28 #else: |
643338ac83c0
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29 -outfmt $out_format |
643338ac83c0
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30 #end if |
643338ac83c0
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31 -num_threads 8 |
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32 #if $adv_opts.adv_opts_selector=="advanced": |
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33 $adv_opts.filter_query |
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34 -matrix $adv_opts.matrix |
643338ac83c0
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35 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string |
643338ac83c0
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36 ## Note -max_target_seqs overrides -num_descriptions and -num_alignments |
643338ac83c0
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37 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): |
643338ac83c0
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38 -max_target_seqs $adv_opts.max_hits |
643338ac83c0
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39 #end if |
643338ac83c0
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40 #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): |
643338ac83c0
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41 -word_size $adv_opts.word_size |
643338ac83c0
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42 #end if |
643338ac83c0
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43 ##Ungapped disabled for now - see comments below |
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44 ##$adv_opts.ungapped |
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45 $adv_opts.parse_deflines |
643338ac83c0
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46 ## End of advanced options: |
643338ac83c0
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47 #end if |
643338ac83c0
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48 </command> |
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49 <stdio> |
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50 <!-- Anything other than zero is an error --> |
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51 <exit_code range="1:" /> |
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52 <exit_code range=":-1" /> |
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53 <!-- In case the return code has not been set propery check stderr too --> |
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54 <regex match="Error:" /> |
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9dabbfd73c8a
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peterjc
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55 <regex match="Exception:" /> |
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9d5beacae92b
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56 </stdio> |
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57 <inputs> |
643338ac83c0
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58 <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> |
643338ac83c0
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peterjc
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59 <conditional name="db_opts"> |
643338ac83c0
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60 <param name="db_opts_selector" type="select" label="Subject database/sequences"> |
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9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
peterjc
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61 <option value="db" selected="True">Locally installed BLAST database</option> |
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62 <option value="histdb">BLAST database from your history</option> |
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63 <option value="file">FASTA file from your history (see warning note below)</option> |
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64 </param> |
643338ac83c0
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65 <when value="db"> |
643338ac83c0
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66 <param name="database" type="select" label="Protein BLAST database"> |
643338ac83c0
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67 <options from_file="blastdb_p.loc"> |
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68 <column name="value" index="0"/> |
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69 <column name="name" index="1"/> |
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70 <column name="path" index="2"/> |
643338ac83c0
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71 </options> |
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72 </param> |
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73 <param name="histdb" type="hidden" value="" /> |
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74 <param name="subject" type="hidden" value="" /> |
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75 </when> |
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76 <when value="histdb"> |
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77 <param name="database" type="hidden" value="" /> |
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78 <param name="histdb" type="data" format="blastdbp" label="Protein BLAST database" /> |
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79 <param name="subject" type="hidden" value="" /> |
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80 </when> |
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81 <when value="file"> |
643338ac83c0
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82 <param name="database" type="hidden" value="" /> |
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83 <param name="histdb" type="hidden" value="" /> |
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84 <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> |
643338ac83c0
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85 </when> |
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86 </conditional> |
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87 <param name="blast_type" type="select" display="radio" label="Type of BLAST"> |
643338ac83c0
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88 <option value="blastp">blastp</option> |
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89 <option value="blastp-short">blastp-short</option> |
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90 </param> |
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91 <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> |
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92 <param name="out_format" type="select" label="Output format"> |
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93 <option value="6">Tabular (standard 12 columns)</option> |
1f546099212f
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94 <option value="ext" selected="True">Tabular (extended 24 columns)</option> |
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95 <option value="5">BLAST XML</option> |
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96 <option value="0">Pairwise text</option> |
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97 <option value="0 -html">Pairwise HTML</option> |
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98 <option value="2">Query-anchored text</option> |
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99 <option value="2 -html">Query-anchored HTML</option> |
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100 <option value="4">Flat query-anchored text</option> |
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101 <option value="4 -html">Flat query-anchored HTML</option> |
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102 <!-- |
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103 <option value="-outfmt 11">BLAST archive format (ASN.1)</option> |
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104 --> |
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105 </param> |
643338ac83c0
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106 <conditional name="adv_opts"> |
643338ac83c0
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107 <param name="adv_opts_selector" type="select" label="Advanced Options"> |
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108 <option value="basic" selected="True">Hide Advanced Options</option> |
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109 <option value="advanced">Show Advanced Options</option> |
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110 </param> |
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111 <when value="basic" /> |
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112 <when value="advanced"> |
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113 <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> |
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114 <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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115 <param name="matrix" type="select" label="Scoring matrix"> |
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116 <option value="BLOSUM90">BLOSUM90</option> |
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117 <option value="BLOSUM80">BLOSUM80</option> |
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118 <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option> |
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119 <option value="BLOSUM50">BLOSUM50</option> |
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120 <option value="BLOSUM45">BLOSUM45</option> |
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121 <option value="PAM250">PAM250</option> |
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122 <option value="PAM70">PAM70</option> |
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123 <option value="PAM30">PAM30</option> |
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124 </param> |
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125 <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> |
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126 <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> |
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127 <validator type="in_range" min="0" /> |
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128 </param> |
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129 <!-- I'd like word_size to be optional, with minimum 2 for blastp --> |
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130 <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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131 <validator type="in_range" min="0" /> |
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132 </param> |
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133 <!-- |
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134 Can't use '-ungapped' on its own, error back is: |
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135 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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136 Tried using '-ungapped -comp_based_stats F' and blastp crashed with 'Attempt to access NULL pointer.' |
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137 <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" /> |
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138 --> |
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139 <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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140 </when> |
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141 </conditional> |
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142 </inputs> |
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143 <outputs> |
9
9dabbfd73c8a
Uploaded v0.0.19, adds wrappers for rpsblast and rpstblastn with new blastdb_d.loc file for their protein domain database.
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144 <data name="output1" format="tabular" label="${blast_type.value_label} on ${on_string}"> |
3
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145 <change_format> |
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146 <when input="out_format" value="0" format="txt"/> |
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147 <when input="out_format" value="0 -html" format="html"/> |
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148 <when input="out_format" value="2" format="txt"/> |
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149 <when input="out_format" value="2 -html" format="html"/> |
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150 <when input="out_format" value="4" format="txt"/> |
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151 <when input="out_format" value="4 -html" format="html"/> |
643338ac83c0
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152 <when input="out_format" value="5" format="blastxml"/> |
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153 </change_format> |
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154 </data> |
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155 </outputs> |
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156 <tests> |
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157 <test> |
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158 <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> |
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159 <param name="db_opts_selector" value="file" /> |
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160 <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" /> |
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161 <param name="database" value="" /> |
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162 <param name="evalue_cutoff" value="1e-8" /> |
643338ac83c0
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163 <param name="blast_type" value="blastp" /> |
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164 <param name="out_format" value="5" /> |
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Uploaded v0.0.12b, same code but moving folders around to match all my other tools and make future development simpler.
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165 <param name="adv_opts_selector" value="advanced" /> |
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166 <param name="filter_query" value="False" /> |
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167 <param name="matrix" value="BLOSUM62" /> |
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168 <param name="max_hits" value="0" /> |
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169 <param name="word_size" value="0" /> |
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170 <param name="parse_deflines" value="True" /> |
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171 <output name="output1" file="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" /> |
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172 </test> |
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173 <test> |
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174 <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> |
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175 <param name="db_opts_selector" value="file" /> |
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176 <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" /> |
643338ac83c0
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177 <param name="database" value="" /> |
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178 <param name="evalue_cutoff" value="1e-8" /> |
643338ac83c0
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179 <param name="blast_type" value="blastp" /> |
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180 <param name="out_format" value="6" /> |
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181 <param name="adv_opts_selector" value="advanced" /> |
643338ac83c0
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182 <param name="filter_query" value="False" /> |
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183 <param name="matrix" value="BLOSUM62" /> |
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184 <param name="max_hits" value="0" /> |
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185 <param name="word_size" value="0" /> |
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186 <param name="parse_deflines" value="True" /> |
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187 <output name="output1" file="blastp_four_human_vs_rhodopsin.tabular" ftype="tabular" /> |
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188 </test> |
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189 <test> |
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190 <param name="query" value="four_human_proteins.fasta" ftype="fasta" /> |
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191 <param name="db_opts_selector" value="file" /> |
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192 <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" /> |
643338ac83c0
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193 <param name="database" value="" /> |
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194 <param name="evalue_cutoff" value="1e-8" /> |
643338ac83c0
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195 <param name="blast_type" value="blastp" /> |
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196 <param name="out_format" value="ext" /> |
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197 <param name="adv_opts_selector" value="advanced" /> |
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198 <param name="filter_query" value="False" /> |
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199 <param name="matrix" value="BLOSUM62" /> |
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200 <param name="max_hits" value="0" /> |
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201 <param name="word_size" value="0" /> |
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202 <param name="parse_deflines" value="True" /> |
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203 <output name="output1" file="blastp_four_human_vs_rhodopsin_ext.tabular" ftype="tabular" /> |
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204 </test> |
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205 <test> |
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206 <param name="query" value="rhodopsin_proteins.fasta" ftype="fasta" /> |
643338ac83c0
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207 <param name="db_opts_selector" value="file" /> |
643338ac83c0
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208 <param name="subject" value="four_human_proteins.fasta" ftype="fasta" /> |
643338ac83c0
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209 <param name="database" value="" /> |
643338ac83c0
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210 <param name="evalue_cutoff" value="1e-8" /> |
643338ac83c0
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211 <param name="blast_type" value="blastp" /> |
643338ac83c0
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212 <param name="out_format" value="6" /> |
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213 <param name="adv_opts_selector" value="basic" /> |
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214 <output name="output1" file="blastp_rhodopsin_vs_four_human.tabular" ftype="tabular" /> |
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215 </test> |
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216 </tests> |
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217 <help> |
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218 |
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219 .. class:: warningmark |
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220 |
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221 **Note**. Database searches may take a substantial amount of time. |
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222 For large input datasets it is advisable to allow overnight processing. |
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223 |
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224 ----- |
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225 |
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226 **What it does** |
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227 |
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228 Search a *protein database* using a *protein query*, |
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229 using the NCBI BLAST+ blastp command line tool. |
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230 |
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231 .. class:: warningmark |
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232 |
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233 You can also search against a FASTA file of subject protein |
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234 sequences. This is *not* advised because it is slower (only one |
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235 CPU is used), but more importantly gives e-values for pairwise |
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236 searches (very small e-values which will look overly signficiant). |
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237 In most cases you should instead turn the other FASTA file into a |
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238 database first using *makeblastdb* and search against that. |
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239 |
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240 ----- |
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241 |
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242 **Output format** |
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243 |
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244 Because Galaxy focuses on processing tabular data, the default output of this |
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245 tool is tabular. The standard BLAST+ tabular output contains 12 columns: |
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246 |
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247 ====== ========= ============================================ |
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248 Column NCBI name Description |
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249 ------ --------- -------------------------------------------- |
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250 1 qseqid Query Seq-id (ID of your sequence) |
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251 2 sseqid Subject Seq-id (ID of the database hit) |
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252 3 pident Percentage of identical matches |
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253 4 length Alignment length |
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254 5 mismatch Number of mismatches |
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255 6 gapopen Number of gap openings |
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256 7 qstart Start of alignment in query |
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257 8 qend End of alignment in query |
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258 9 sstart Start of alignment in subject (database hit) |
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259 10 send End of alignment in subject (database hit) |
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260 11 evalue Expectation value (E-value) |
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261 12 bitscore Bit score |
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262 ====== ========= ============================================ |
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263 |
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264 The BLAST+ tools can optionally output additional columns of information, |
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265 but this takes longer to calculate. Most (but not all) of these columns are |
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266 included by selecting the extended tabular output. The extra columns are |
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267 included *after* the standard 12 columns. This is so that you can write |
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268 workflow filtering steps that accept either the 12 or 24 column tabular |
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269 BLAST output. Galaxy now uses this extended 24 column output by default. |
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270 |
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271 ====== ============= =========================================== |
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272 Column NCBI name Description |
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273 ------ ------------- ------------------------------------------- |
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274 13 sallseqid All subject Seq-id(s), separated by a ';' |
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275 14 score Raw score |
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276 15 nident Number of identical matches |
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277 16 positive Number of positive-scoring matches |
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278 17 gaps Total number of gaps |
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279 18 ppos Percentage of positive-scoring matches |
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280 19 qframe Query frame |
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281 20 sframe Subject frame |
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282 21 qseq Aligned part of query sequence |
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283 22 sseq Aligned part of subject sequence |
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284 23 qlen Query sequence length |
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285 24 slen Subject sequence length |
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286 ====== ============= =========================================== |
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287 |
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288 The third option is BLAST XML output, which is designed to be parsed by |
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289 another program, and is understood by some Galaxy tools. |
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290 |
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291 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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292 The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. |
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293 The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. |
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294 The two query anchored outputs show a multiple sequence alignment between the query and all the matches, |
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295 and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). |
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296 |
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297 ------- |
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298 |
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299 **References** |
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300 |
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301 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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302 |
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303 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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304 |
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305 </help> |
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306 </tool> |