Mercurial > repos > devteam > ncbi_blast_plus

annotate tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml @ 27:6f8ea4b9a2c4 draft

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"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
author peterjc
date Wed, 09 Sep 2020 15:32:17 +0000
parents 2889433c7ae1
children 87a7ee4cb36f
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1 <tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Extract sequence(s) from BLAST database</description>
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3 <macros>
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4 <token name="@BINARY@">blastdbcmd</token>
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5 <import>ncbi_macros.xml</import>
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6 </macros>
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7 <expand macro="preamble" />
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8 <command detect_errors="aggressive" strict="true">
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9 ## The command is a Cheetah template which allows some Python based syntax.
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10 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
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11 blastdbcmd
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12 @DBCMD_OPTS@
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14 ##TODO: What about -ctrl_a and -target_only as advanced options?
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16 #if $id_opts.id_type=="file":
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17 -entry_batch '$id_opts.entries'
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18 #else:
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19 ##Perform some simple search/replaces to remove whitespace
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20 ##and make it comma separated. Quoted so don't escape pipes.
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21 -entry "$id_opts.entries.replace('\r',',').replace('\n',',').replace(' ','').replace(',,',',').replace(',,',',').strip(',')"
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22 #end if
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24 ##When building a BLAST database, to ensure unique IDs makeblastdb will
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25 ##do things like turning a FASTA entry with ID of ERP44 into lcl|ERP44
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26 ##(if using -parse_seqids) or simply assign it an ID using the record
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27 ##number like gnl|BL_ORD_ID|123 (to cope with duplicate IDs in the FASTA
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28 ##file). In -parse_seqids mode, a duplicate FASTA ID gives an error.
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29 ##
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30 ##The BLAST plain text and XML output will contain these BLAST IDs, but
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31 ##the tabular output does not (at least, not in BLAST 2.2.25+).
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32 ##Therefore in general, Galaxy users won't care about the (internal)
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33 ##BLAST identifiers.
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34 ##
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35 ##The blastdbcmd FASTA output will also contain these IDs, but in the
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36 ##context of the BLAST tabular output they are not helpful. Therefore
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37 ##to recover the original ID as used in the FASTA file for makeblastdb
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38 ##we need a litte post processing.
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39 ##
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40 ##We remove the NCBI's lcl|... or gnl|BL_ORD_ID|123 prefixes
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41 ##using sed, however the exact syntax differs for Mac OS X's sed
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42
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43 #if str($outfmt)=="blastid":
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44 -out '$seq'
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45 #else if sys.platform == "darwin":
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46 | sed -E 's/^&gt;(lcl\||gnl\|BL_ORD_ID\|[0-9]* )/&gt;/1' &gt; "$seq"
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47 #else:
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48 | sed 's/&gt;\(lcl|\|gnl|BL_ORD_ID|[0-9]* \)/&gt;/1' &gt; "$seq"
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49 #end if
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50 </command>
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51 <inputs>
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52 <expand macro="input_conditional_choose_db_type" />
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53 <conditional name="id_opts">
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54 <param name="id_type" type="select" label="Type of identifier list">
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55 <option value="file">From file</option>
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56 <option value="prompt">User entered</option>
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57 </param>
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58 <when value="file">
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59 <param name="entries" argument="-entry_batch" type="data" format="txt,tabular" label="Sequence identifier(s)" help="Plain text file with one ID per line, optionally with space separated range, strand, and algorithm."/>
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60 </when>
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61 <when value="prompt">
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62 <param name="entries" argument="-entry" type="text" optional="false" area="true" size="10x30" label="Sequence identifier(s)" help="Comma or new line separated list"/>
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63 </when>
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64 </conditional>
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65 <param name="outfmt" type="select" label="Output format">
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66 <option value="original">FASTA with original identifiers</option>
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67 <option value="blastid">FASTA with BLAST assigned identifiers</option>
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68 </param>
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69 </inputs>
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70 <outputs>
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72 <data name="seq" format="fasta" label="Sequences from blastdbcmd @ON_DBCMD_OPTS@">
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73 </data>
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74 </outputs>
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75 <tests>
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76 <test>
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77 <param name="db_opts|db_type" value="prot" />
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78 <param name="db_opts|db_origin|database" value="four_human_proteins" />
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79 <param name="db_opts|db_origin|db_origin_selector" value="db" />
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80 <param name="id_opts|id_type" value="prompt" />
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81 <param name="id_opts|entries" value="all" />
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82 <param name="outfmt" value="original" />
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83 <output name="seq" file="four_human_proteins.fasta" ftype="fasta" />
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84 </test>
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85 <test>
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86 <!-- This used to recover the original FASTA file, but had GI numbers -->
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87 <param name="db_opts|db_type" value="nucl" />
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88 <param name="db_opts|db_origin|database" value="rhodopsin_nucs" />
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89 <param name="id_opts|id_type" value="prompt" />
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90 <param name="id_opts|entries" value="all" />
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91 <param name="outfmt" value="original" />
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92 <output name="seq" file="rhodopsin_nucs.no_gi.fasta" ftype="fasta" />
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93 </test>
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94 <test>
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95 <!-- This uses various start end frame combinations but all recover full sequence -->
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96 <param name="db_opts|db_type" value="nucl" />
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97 <param name="db_opts|db_origin|database" value="rhodopsin_nucs" />
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98 <param name="id_opts|id_type" value="file" />
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99 <param name="id_opts|entries" value="rhodopsin_nucs.blastdbcmd.txt" ftype="txt" />
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100 <param name="outfmt" value="original" />
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101 <output name="seq" file="rhodopsin_nucs.no_gi.fasta" ftype="fasta" />
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102 </test>
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103 <test>
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104 <param name="db_opts|db_type" value="nucl" />
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105 <param name="db_opts|db_origin|database" value="rhodopsin_nucs" />
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106 <param name="id_opts|id_type" value="prompt" />
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107 <param name="id_opts|entries" value="U59921.1" />
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108 <param name="outfmt" value="original" />
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109 <output name="seq" file="rhodopsin_bufo.fasta" ftype="fasta" />
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110 </test>
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111 <test>
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112 <param name="db_opts|db_type" value="nucl" />
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113 <!-- look in two databases for this entry -->
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114 <param name="db_opts|db_origin|database" value="rhodopsin_nucs,three_human_mRNA" />
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115 <param name="id_opts|id_type" value="prompt" />
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116 <param name="id_opts|entries" value="gi|2734705|gb|U59921.1|BBU59921" />
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117 <param name="outfmt" value="original" />
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118 <output name="seq" file="rhodopsin_bufo.fasta" ftype="fasta" />
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119 </test>
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120 </tests>
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121 <help>
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122
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123 **What it does**
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124
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125 Extracts FASTA formatted sequences from a BLAST database
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126 using the NCBI BLAST+ blastdbcmd command line tool.
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127
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128 When giving a text file of entries, use one line per sequence.
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129 Optional valies should be space separate - the simplest syntax
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130 is ``identifier start-end`` (where ``end`` can be just ``-``),
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131 or ``identifier start-end strand`` (wheere the strand given as
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132 either ``+`` or ``-``).
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133
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134 .. class:: warningmark
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135
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136 **BLAST assigned identifiers**
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137
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138 When a BLAST database is constructed from a FASTA file, the
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139 original identifiers can be replaced with BLAST assigned
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140 identifiers, partly to ensure uniqueness. e.g. Sometimes
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141 a prefix of 'lcl|' is added (lcl is short for local),
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142 or an arbitrary name starting 'gnl|BL_ORD_ID|' is created.
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143
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144 If you are using the tabular output from BLAST, it will contain
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145 the original identifiers - not the BLAST assigned identifiers
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146 suitable for use with the blastdbcmd tool.
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147
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148 If you are using the XML or plain text output, this will also
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149 contain the BLAST assigned identifiers. However, this means
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150 getting a list of BLAST assigned identifiers isn't straightforward.
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151
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152 -------
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153
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154 @CLI_OPTIONS@
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155
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156 -------
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157
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158 **References**
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159
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160 If you use this Galaxy tool in work leading to a scientific publication please
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161 cite the following papers:
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162
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163 @REFERENCES@
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164 </help>
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165 <expand macro="blast_citations" />
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166 </tool>