Mercurial > repos > edward-kirton > blast
annotate blast/blastx.xml @ 0:f3ac34855f5e default tip
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author | edward-kirton |
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date | Tue, 07 Jun 2011 17:30:11 -0400 |
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1 <tool id="blastx" name="blastx" version="0.0.1"> |
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2 <description>Search protein database with translated nucleotide query sequence(s)</description> |
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3 <command> |
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4 ## The command is a Cheetah template which allows some Python based syntax. |
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5 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces |
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6 blastx |
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7 -query "$query" |
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8 #if $db_opts.db_opts_selector == "db": |
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9 -db "$db_opts.database" |
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10 #elif $db_opts.db_opts_selector == "user_db": |
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11 -db "$db_opts.db" |
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12 #else: |
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13 -subject "$db_opts.subject" |
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14 #end if |
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15 -evalue $evalue_cutoff |
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16 -out $output1 |
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17 -outfmt "$out_format" |
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18 #if $adv_opts.adv_opts_selector=="advanced": |
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19 $adv_opts.filter_query |
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20 $adv_opts.strand |
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21 -matrix $adv_opts.matrix |
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22 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string |
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23 ## Note -max_target_seqs overrides -num_descriptions and -num_alignments |
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24 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): |
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25 -max_target_seqs $adv_opts.max_hits |
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26 #end if |
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27 #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): |
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28 -word_size $adv_opts.word_size |
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29 #end if |
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30 $adv_opts.ungapped |
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31 $adv_opts.parse_deflines |
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32 ## End of advanced options: |
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33 #end if |
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34 </command> |
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35 <inputs> |
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36 <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> |
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37 <conditional name="db_opts"> |
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38 <param name="db_opts_selector" type="select" label="Subject database/sequences"> |
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39 <option value="db" selected="True">Precompiled BLAST Database</option> |
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40 <option value="user_db">BLAST Database in your History</option> |
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41 <option value="fasta">FASTA file</option> |
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42 </param> |
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43 <when value="db"> |
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44 <param name="database" type="select" label="Precompiled Protein BLAST database"> |
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45 <!-- The BLAST loc file has three columns: |
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46 column 0 is an identifier (not used), |
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47 column 1 is the caption (show this to the user), |
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48 column 2 is the database path (given to BLAST+) --> |
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49 <options from_file="blastdb_p.loc"> |
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50 <column name="name" index="1"/> |
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51 <column name="value" index="2"/> |
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52 </options> |
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53 </param> |
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54 <param name="subject" type="hidden" value="" /> |
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55 </when> |
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56 <when value="user_db"> |
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57 <param name="database" type="hidden" value="" /> |
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58 <param name="db" type="data" format="blastdb" label="Blast DB" /> |
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59 </when> |
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60 <when value="fasta"> |
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61 <param name="database" type="hidden" value="" /> |
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62 <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> |
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63 </when> |
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64 </conditional> |
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65 <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> |
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66 <param name="out_format" type="select" label="Output format"> |
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67 <option value="6" selected="True">Tabular (standard 12 columns)</option> |
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68 <option value="6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq">Tabular (extended 22 columns)</option> |
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69 <option value="5">BLAST XML</option> |
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70 <option value="0">Pairwise text</option> |
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71 <option value="0 -html">Pairwise HTML</option> |
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72 <option value="2">Query-anchored text</option> |
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73 <option value="2 -html">Query-anchored HTML</option> |
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74 <option value="4">Flat query-anchored text</option> |
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75 <option value="4 -html">Flat query-anchored HTML</option> |
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76 <!-- |
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77 <option value="-outfmt 11">BLAST archive format (ASN.1)</option> |
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78 --> |
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79 </param> |
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80 <conditional name="adv_opts"> |
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81 <param name="adv_opts_selector" type="select" label="Advanced Options"> |
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82 <option value="basic" selected="True">Hide Advanced Options</option> |
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83 <option value="advanced">Show Advanced Options</option> |
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84 </param> |
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85 <when value="basic" /> |
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86 <when value="advanced"> |
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87 <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> |
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88 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> |
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89 <param name="strand" type="select" label="Query strand(s) to search against database/subject"> |
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90 <option value="-strand both">Both</option> |
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91 <option value="-strand plus">Plus (forward)</option> |
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92 <option value="-strand minus">Minus (reverse complement)</option> |
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93 </param> |
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94 <param name="matrix" type="select" label="Scoring matrix"> |
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95 <option value="BLOSUM90">BLOSUM90</option> |
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96 <option value="BLOSUM80">BLOSUM80</option> |
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97 <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option> |
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98 <option value="BLOSUM50">BLOSUM50</option> |
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99 <option value="BLOSUM45">BLOSUM45</option> |
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100 <option value="PAM250">PAM250</option> |
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101 <option value="PAM70">PAM70</option> |
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102 <option value="PAM30">PAM30</option> |
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103 </param> |
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104 <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> |
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105 <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> |
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106 <validator type="in_range" min="0" /> |
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107 </param> |
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108 <!-- I'd like word_size to be optional, with minimum 2 for blastx --> |
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109 <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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110 <validator type="in_range" min="0" /> |
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111 </param> |
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112 <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> |
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113 <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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114 </when> |
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115 </conditional> |
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116 </inputs> |
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117 <outputs> |
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118 <data name="output1" format="tabular" label="blastx on ${db_opts.db_opts_selector}"> |
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119 <change_format> |
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120 <when input="out_format" value="0" format="txt"/> |
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121 <when input="out_format" value="0 -html" format="html"/> |
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122 <when input="out_format" value="2" format="txt"/> |
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123 <when input="out_format" value="2 -html" format="html"/> |
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124 <when input="out_format" value="4" format="txt"/> |
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125 <when input="out_format" value="4 -html" format="html"/> |
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126 <when input="out_format" value="5" format="blastxml"/> |
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127 </change_format> |
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128 </data> |
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129 </outputs> |
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130 <requirements> |
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131 <requirement type="binary">blastx</requirement> |
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132 </requirements> |
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133 <tests> |
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134 </tests> |
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135 <help> |
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136 |
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137 .. class:: warningmark |
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138 |
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139 **Note**. Database searches may take a substantial amount of time. |
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140 For large input datasets it is advisable to allow overnight processing. |
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141 |
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142 ----- |
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143 |
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144 **What it does** |
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145 |
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146 Search a *protein database* using a *translated nucleotide query*, |
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147 using the NCBI BLAST+ blastx command line tool. |
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148 |
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149 ----- |
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150 |
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151 **Output format** |
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152 |
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153 Because Galaxy focuses on processing tabular data, the default output of this |
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154 tool is tabular. The standard BLAST+ tabular output contains 12 columns: |
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155 |
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156 ====== ========= ============================================ |
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157 Column NCBI name Description |
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158 ------ --------- -------------------------------------------- |
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159 1 qseqid Query Seq-id (ID of your sequence) |
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160 2 sseqid Subject Seq-id (ID of the database hit) |
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161 3 pident Percentage of identical matches |
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162 4 length Alignment length |
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163 5 mismatch Number of mismatches |
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164 6 gapopen Number of gap openings |
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165 7 qstart Start of alignment in query |
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166 8 qend End of alignment in query |
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167 9 sstart Start of alignment in subject (database hit) |
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168 10 send End of alignment in subject (database hit) |
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169 11 evalue Expectation value (E-value) |
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170 12 bitscore Bit score |
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171 ====== ========= ============================================ |
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172 |
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173 The BLAST+ tools can optionally output additional columns of information, |
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174 but this takes longer to calculate. Most (but not all) of these columns are |
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175 included by selecting the extended tabular output. The extra columns are |
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176 included *after* the standard 12 columns. This is so that you can write |
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177 workflow filtering steps that accept either the 12 or 22 column tabular |
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178 BLAST output. |
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179 |
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180 ====== ============= =========================================== |
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181 Column NCBI name Description |
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182 ------ ------------- ------------------------------------------- |
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183 13 sallseqid All subject Seq-id(s), separated by a ';' |
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184 14 score Raw score |
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185 15 nident Number of identical matches |
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186 16 positive Number of positive-scoring matches |
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187 17 gaps Total number of gaps |
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188 18 ppos Percentage of positive-scoring matches |
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189 19 qframe Query frame |
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190 20 sframe Subject frame |
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191 21 qseq Aligned part of query sequence |
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192 22 sseq Aligned part of subject sequence |
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193 ====== ============= =========================================== |
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194 |
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195 The third option is BLAST XML output, which is designed to be parsed by |
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196 another program, and is understood by some Galaxy tools. |
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197 |
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198 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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199 The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. |
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200 The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. |
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201 The two query anchored outputs show a multiple sequence alignment between the query and all the matches, |
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202 and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). |
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203 |
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204 ------- |
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205 |
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206 **References** |
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207 |
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208 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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209 |
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210 </help> |
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211 </tool> |