Mercurial > repos > devteam > ncbi_blast_plus

annotate tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml @ 23:9e483194ebf6 draft

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planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit befaf16290a437209109c06c20d0deb170925d16-dirty
author peterjc
date Fri, 15 Sep 2017 07:52:22 -0400
parents 771b554bc85d
children 3b4efe26da79
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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856b73016ba1 v0.1.05 - Update citation information now GigaScience paper is out
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1 <tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="@WRAPPER_VERSION@">
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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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e98f6bd363ba planemo upload for repository https://github.com/peterjc/galaxy_blast/tools/ncbi_blast_plus commit a567843bb239ee8faec72eb7e52f3b5aa3191631
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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 -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}"
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12
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13 ##TODO: What about -ctrl_a and -target_only as advanced options?
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14
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15 #if $id_opts.id_type=="file":
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16 -entry_batch '$id_opts.entries'
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17 #else:
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18 ##Perform some simple search/replaces to remove whitespace
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19 ##and make it comma separated. Quoted so don't escape pipes.
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20 -entry "$id_opts.entries.replace('\r',',').replace('\n',',').replace(' ','').replace(',,',',').replace(',,',',').strip(',')"
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21 #end if
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22
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23 ##When building a BLAST database, to ensure unique IDs makeblastdb will
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24 ##do things like turning a FASTA entry with ID of ERP44 into lcl|ERP44
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25 ##(if using -parse_seqids) or simply assign it an ID using the record
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26 ##number like gnl|BL_ORD_ID|123 (to cope with duplicate IDs in the FASTA
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27 ##file). In -parse_seqids mode, a duplicate FASTA ID gives an error.
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28 ##
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29 ##The BLAST plain text and XML output will contain these BLAST IDs, but
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30 ##the tabular output does not (at least, not in BLAST 2.2.25+).
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31 ##Therefore in general, Galaxy users won't care about the (internal)
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32 ##BLAST identifiers.
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33 ##
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34 ##The blastdbcmd FASTA output will also contain these IDs, but in the
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35 ##context of the BLAST tabular output they are not helpful. Therefore
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36 ##to recover the original ID as used in the FASTA file for makeblastdb
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37 ##we need a litte post processing.
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38 ##
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39 ##We remove the NCBI's lcl|... or gnl|BL_ORD_ID|123 prefixes
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40 ##using sed, however the exact syntax differs for Mac OS X's sed
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41
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42 #if str($outfmt)=="blastid":
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43 -out '$seq'
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44 #else if sys.platform == "darwin":
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45 | sed -E 's/^&gt;(lcl\||gnl\|BL_ORD_ID\|[0-9]* )/&gt;/1' &gt; "$seq"
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46 #else:
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47 | sed 's/&gt;\(lcl|\|gnl|BL_ORD_ID|[0-9]* \)/&gt;/1' &gt; "$seq"
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48 #end if
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49 </command>
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50 <inputs>
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51 <expand macro="input_conditional_choose_db_type" />
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52 <conditional name="id_opts">
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53 <param name="id_type" type="select" label="Type of identifier list">
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54 <option value="file">From file</option>
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55 <option value="prompt">User entered</option>
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56 </param>
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57 <when value="file">
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58 <param name="entries" argument="-entry_batch" type="data" format="txt,tabular" label="Sequence identifier(s)" help="Plain text file with one ID per line (i.e. single column tabular file)"/>
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59 </when>
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60 <when value="prompt">
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61 <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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62 </when>
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63 </conditional>
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64 <param name="outfmt" type="select" label="Output format">
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65 <option value="original">FASTA with original identifiers</option>
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66 <option value="blastid">FASTA with BLAST assigned identifiers</option>
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67 </param>
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68 </inputs>
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69 <outputs>
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70 <data name="seq" format="fasta" label="Sequences from ${db_opts.database.fields.name}" />
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71 </outputs>
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72 <tests>
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73 <test>
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74 <param name="db_opts|db_type" value="prot" />
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75 <param name="db_opts|database" value="four_human_proteins" />
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76 <param name="id_opts|id_type" value="prompt" />
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77 <param name="id_opts|entries" value="all" />
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78 <param name="outfmt" value="original" />
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79 <output name="seq" file="four_human_proteins.fasta" ftype="fasta" />
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80 </test>
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81 <test>
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82 <!-- This used to recover the original FASTA file, but had GI numbers -->
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83 <param name="db_opts|db_type" value="nucl" />
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84 <param name="db_opts|database" value="rhodopsin_nucs" />
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85 <param name="id_opts|id_type" value="prompt" />
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86 <param name="id_opts|entries" value="all" />
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87 <param name="outfmt" value="original" />
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88 <output name="seq" file="rhodopsin_nucs.no_gi.fasta" ftype="fasta" />
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89 </test>
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90 <test>
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91 <param name="db_opts|db_type" value="nucl" />
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92 <param name="db_opts|database" value="rhodopsin_nucs" />
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93 <param name="id_opts|id_type" value="prompt" />
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94 <param name="id_opts|entries" value="U59921.1" />
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95 <param name="outfmt" value="original" />
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96 <output name="seq" file="rhodopsin_bufo.fasta" ftype="fasta" />
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97 </test>
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98 <test>
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99 <param name="db_opts|db_type" value="nucl" />
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100 <param name="db_opts|database" value="rhodopsin_nucs" />
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101 <param name="id_opts|id_type" value="prompt" />
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102 <param name="id_opts|entries" value="gi|2734705|gb|U59921.1|BBU59921" />
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103 <param name="outfmt" value="original" />
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104 <output name="seq" file="rhodopsin_bufo.fasta" ftype="fasta" />
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105 </test>
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106 </tests>
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107 <help>
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108
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109 **What it does**
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110
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111 Extracts FASTA formatted sequences from a BLAST database
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112 using the NCBI BLAST+ blastdbcmd command line tool.
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113
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114 .. class:: warningmark
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115
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116 **BLAST assigned identifiers**
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117
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118 When a BLAST database is constructed from a FASTA file, the
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119 original identifiers can be replaced with BLAST assigned
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120 identifiers, partly to ensure uniqueness. e.g. Sometimes
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121 a prefix of 'lcl|' is added (lcl is short for local),
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122 or an arbitrary name starting 'gnl|BL_ORD_ID|' is created.
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123
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124 If you are using the tabular output from BLAST, it will contain
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125 the original identifiers - not the BLAST assigned identifiers
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126 suitable for use with the blastdbcmd tool.
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127
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128 If you are using the XML or plain text output, this will also
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129 contain the BLAST assigned identifiers. However, this means
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130 getting a list of BLAST assigned identifiers isn't straightforward.
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131
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132 -------
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133
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134 **References**
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135
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136 If you use this Galaxy tool in work leading to a scientific publication please
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137 cite the following papers:
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138
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139 @REFERENCES@
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140 </help>
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141 <expand macro="blast_citations" />
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142 </tool>