Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_rpstblastn_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 |
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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_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="0.0.3"> |
9dabbfd73c8a
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peterjc
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2 <description>Search protein domain database (PSSMs) with translated nucleotide query sequence(s)</description> |
9dabbfd73c8a
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3 <!-- If job splitting is enabled, break up the query file into parts --> |
9dabbfd73c8a
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peterjc
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4 <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism> |
9dabbfd73c8a
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5 <requirements> |
9dabbfd73c8a
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6 <requirement type="binary">rpstblastn</requirement> |
9dabbfd73c8a
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peterjc
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7 <requirement type="package" version="2.2.26+">blast+</requirement> |
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8 </requirements> |
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9 <version_command>rpstblastn -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 |
9dabbfd73c8a
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13 rpstblastn |
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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 #end if |
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20 -evalue $evalue_cutoff |
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21 -out "$output1" |
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22 ##Set the extended list here so if/when we add things, saved workflows are not affected |
9dabbfd73c8a
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23 #if str($out_format)=="ext": |
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24 -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" |
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25 #else: |
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26 -outfmt $out_format |
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27 #end if |
9dabbfd73c8a
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28 ##Seems rpstblastn does not currently support multiple threads :( |
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29 ##-num_threads 8 |
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30 #if $adv_opts.adv_opts_selector=="advanced": |
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31 $adv_opts.filter_query |
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32 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string |
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33 ## Note -max_target_seqs overrides -num_descriptions and -num_alignments |
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34 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): |
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35 -max_target_seqs $adv_opts.max_hits |
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36 #end if |
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37 #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): |
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38 -word_size $adv_opts.word_size |
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39 #end if |
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40 $adv_opts.parse_deflines |
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41 ## End of advanced options: |
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42 #end if |
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43 </command> |
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44 <stdio> |
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45 <!-- Anything other than zero is an error --> |
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46 <exit_code range="1:" /> |
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47 <exit_code range=":-1" /> |
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48 <!-- In case the return code has not been set propery check stderr too --> |
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49 <regex match="Error:" /> |
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50 <regex match="Exception:" /> |
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51 </stdio> |
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52 <inputs> |
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53 <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> |
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54 <conditional name="db_opts"> |
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55 <param name="db_opts_selector" type="select" label="Protein domain database (PSSM)"> |
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56 <option value="db" selected="True">Locally installed BLAST database</option> |
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57 <!-- TODO - define new datatype |
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58 <option value="histdb">BLAST protein domain database from your history</option> |
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59 --> |
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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 domain database"> |
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63 <options from_file="blastdb_d.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 <!-- TODO - define new datatype |
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73 <when value="histdb"> |
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74 <param name="database" type="hidden" value="" /> |
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75 <param name="histdb" type="data" format="blastdbd" label="Protein domain database" /> |
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76 <param name="subject" type="hidden" value="" /> |
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77 </when> |
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78 --> |
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79 </conditional> |
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80 <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> |
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81 <param name="out_format" type="select" label="Output format"> |
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82 <option value="6">Tabular (standard 12 columns)</option> |
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83 <option value="ext" selected="True">Tabular (extended 24 columns)</option> |
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84 <option value="5">BLAST XML</option> |
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85 <option value="0">Pairwise text</option> |
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86 <option value="0 -html">Pairwise HTML</option> |
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87 <option value="2">Query-anchored text</option> |
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88 <option value="2 -html">Query-anchored HTML</option> |
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89 <option value="4">Flat query-anchored text</option> |
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90 <option value="4 -html">Flat query-anchored HTML</option> |
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91 <!-- |
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92 <option value="-outfmt 11">BLAST archive format (ASN.1)</option> |
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93 --> |
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94 </param> |
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95 <conditional name="adv_opts"> |
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96 <param name="adv_opts_selector" type="select" label="Advanced Options"> |
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97 <option value="basic" selected="True">Hide Advanced Options</option> |
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98 <option value="advanced">Show Advanced Options</option> |
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99 </param> |
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100 <when value="basic" /> |
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101 <when value="advanced"> |
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102 <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> |
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103 <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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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 rpsblast --> |
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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="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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113 </when> |
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114 </conditional> |
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115 </inputs> |
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116 <outputs> |
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117 <data name="output1" format="tabular" label="rpstblastn on ${on_string}"> |
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118 <change_format> |
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119 <when input="out_format" value="0" format="txt"/> |
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120 <when input="out_format" value="0 -html" format="html"/> |
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121 <when input="out_format" value="2" format="txt"/> |
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122 <when input="out_format" value="2 -html" format="html"/> |
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123 <when input="out_format" value="4" format="txt"/> |
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124 <when input="out_format" value="4 -html" format="html"/> |
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125 <when input="out_format" value="5" format="blastxml"/> |
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126 </change_format> |
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127 </data> |
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128 </outputs> |
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129 <help> |
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130 |
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131 .. class:: warningmark |
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132 |
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133 **Note**. Database searches may take a substantial amount of time. |
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134 For large input datasets it is advisable to allow overnight processing. |
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135 |
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136 ----- |
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137 |
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138 **What it does** |
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139 |
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140 Search a *protein domain database* using a *nucleotide query*, |
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141 using the NCBI BLAST+ rpstblastn command line tool. |
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142 |
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143 The protein domain databases use position-specific scoring matrices |
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144 (PSSMs) and are available for a number of domain collections including: |
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145 |
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146 *CDD* - NCBI curarated meta-collection of domains, see |
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147 http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#NCBI_curated_domains |
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148 |
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149 *Kog* - PSSMs from automatically aligned sequences and sequence |
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150 fragments classified in the KOGs resource, the eukaryotic |
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151 counterpart to COGs, see http://www.ncbi.nlm.nih.gov/COG/new/ |
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152 |
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153 *Cog* - PSSMs from automatically aligned sequences and sequence |
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154 fragments classified in the COGs resource, which focuses primarily |
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155 on prokaryotes, see http://www.ncbi.nlm.nih.gov/COG/new/ |
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156 |
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157 *Pfam* - PSSMs from Pfam-A seed alignment database, see |
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158 http://pfam.sanger.ac.uk/ |
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159 |
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160 *Smart* - PSSMs from SMART domain alignment database, see |
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161 http://smart.embl-heidelberg.de/ |
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162 |
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163 *Tigr* - PSSMs from TIGRFAM database of protein families, see |
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164 http://www.jcvi.org/cms/research/projects/tigrfams/overview/ |
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165 |
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166 *Prk* - PSSms from automatically aligned stable clusters in the |
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167 Protein Clusters database, see |
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168 http://www.ncbi.nlm.nih.gov/proteinclusters?cmd=search&db=proteinclusters |
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169 |
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170 The exact list of domain databases offered will depend on how your |
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171 local Galaxy has been configured. |
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172 |
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173 ----- |
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174 |
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175 **Output format** |
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176 |
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177 Because Galaxy focuses on processing tabular data, the default output of this |
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178 tool is tabular. The standard BLAST+ tabular output contains 12 columns: |
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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 1 qseqid Query Seq-id (ID of your sequence) |
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184 2 sseqid Subject Seq-id (ID of the database hit) |
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185 3 pident Percentage of identical matches |
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186 4 length Alignment length |
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187 5 mismatch Number of mismatches |
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188 6 gapopen Number of gap openings |
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189 7 qstart Start of alignment in query |
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190 8 qend End of alignment in query |
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191 9 sstart Start of alignment in subject (database hit) |
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192 10 send End of alignment in subject (database hit) |
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193 11 evalue Expectation value (E-value) |
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194 12 bitscore Bit score |
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195 ====== ========= ============================================ |
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196 |
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197 The BLAST+ tools can optionally output additional columns of information, |
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198 but this takes longer to calculate. Most (but not all) of these columns are |
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199 included by selecting the extended tabular output. The extra columns are |
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200 included *after* the standard 12 columns. This is so that you can write |
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201 workflow filtering steps that accept either the 12 or 24 column tabular |
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202 BLAST output. Galaxy now uses this extended 24 column output by default. |
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203 |
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204 ====== ============= =========================================== |
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205 Column NCBI name Description |
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206 ------ ------------- ------------------------------------------- |
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207 13 sallseqid All subject Seq-id(s), separated by a ';' |
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208 14 score Raw score |
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209 15 nident Number of identical matches |
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210 16 positive Number of positive-scoring matches |
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211 17 gaps Total number of gaps |
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212 18 ppos Percentage of positive-scoring matches |
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213 19 qframe Query frame |
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214 20 sframe Subject frame |
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215 21 qseq Aligned part of query sequence |
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216 22 sseq Aligned part of subject sequence |
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217 23 qlen Query sequence length |
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218 24 slen Subject sequence length |
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219 ====== ============= =========================================== |
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220 |
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221 The third option is BLAST XML output, which is designed to be parsed by |
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222 another program, and is understood by some Galaxy tools. |
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223 |
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224 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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225 The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. |
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226 The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. |
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227 The two query anchored outputs show a multiple sequence alignment between the query and all the matches, |
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228 and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). |
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229 |
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230 ------- |
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231 |
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232 **References** |
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233 |
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234 Marchler-Bauer A, Bryant SH. CD-Search: protein domain annotations on the fly. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W327-31. |
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235 |
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236 </help> |
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237 </tool> |