Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @ 17:697f40151eaf draft
v0.1.05 - Update citation information now GigaScience paper is out
author | peterjc |
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date | Fri, 04 Sep 2015 09:45:57 -0400 |
parents | b5f1f599d1fb |
children | 7f3c448e119b |
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17
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v0.1.05 - Update citation information now GigaScience paper is out
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1 <tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="@WRAPPER_VERSION@"> |
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2 <description>Search nucleotide database with nucleotide query sequence(s)</description> |
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3 <macros> |
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4 <token name="@BINARY@">blastn</token> |
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5 <import>ncbi_macros.xml</import> |
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6 </macros> |
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7 <expand macro="parallelism" /> |
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8 <expand macro="preamble" /> |
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9 <command> |
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10 ## The command is a Cheetah template which allows some Python based syntax. |
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11 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces |
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12 blastn |
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13 -query "$query" |
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14 @BLAST_DB_SUBJECT@ |
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15 -task $blast_type |
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16 -evalue $evalue_cutoff |
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17 @BLAST_OUTPUT@ |
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18 @THREADS@ |
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19 #if $adv_opts.adv_opts_selector=="advanced": |
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20 $adv_opts.strand |
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21 @ADV_FILTER_QUERY@ |
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22 @ADV_MAX_HITS@ |
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23 @ADV_WORD_SIZE@ |
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24 #if (str($adv_opts.identity_cutoff) and float(str($adv_opts.identity_cutoff)) > 0 ): |
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25 -perc_identity $adv_opts.identity_cutoff |
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26 #end if |
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27 $adv_opts.ungapped |
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28 @ADV_ID_LIST_FILTER@ |
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29 @ADV_QCOV_HSP_PERC@ |
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30 ## End of advanced options: |
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31 #end if |
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32 </command> |
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33 <inputs> |
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34 <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> |
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35 <expand macro="input_conditional_nucleotide_db" /> |
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36 <param name="blast_type" type="select" display="radio" label="Type of BLAST"> |
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37 <option value="megablast">megablast - Traditional megablast used to find very similar (e.g., intraspecies or closely related species) sequences</option> |
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38 <option value="blastn">blastn - Traditional BLASTN requiring an exact match of 11, for somewhat similar sequences</option> |
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39 <option value="blastn-short">blastn-short - BLASTN program optimized for sequences shorter than 50 bases</option> |
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40 <option value="dc-megablast">dc-megablast - Discontiguous megablast used to find more distant (e.g., interspecies) sequences</option> |
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41 <!-- Using BLAST 2.2.24+ this gives an error: |
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42 BLAST engine error: Program type 'vecscreen' not supported |
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43 <option value="vecscreen">vecscreen</option> |
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44 In any case, vecscreen has gone in BLAST+ 2.2.28 |
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45 --> |
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46 <!-- BLAST+ 2.2.28 also offers rmblastn --> |
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47 </param> |
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48 <expand macro="input_evalue" /> |
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49 <expand macro="input_out_format" /> |
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50 <expand macro="advanced_options"> |
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51 <!-- Could use a select (yes, no, other) where other allows setting 'level window linker' --> |
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52 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" /> |
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53 <expand macro="input_strand" /> |
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54 <expand macro="input_max_hits" /> |
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55 <param name="identity_cutoff" type="float" min="0" max="100" value="0" label="Percent identity cutoff (-perc_identity)" help="Use zero for no cutoff" /> |
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56 |
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57 <!-- I'd like word_size to be optional, with minimum 4 for blastn --> |
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58 <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4."> |
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59 <validator type="in_range" min="0" /> |
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60 </param> |
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61 <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> |
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62 <expand macro="input_parse_deflines" /> |
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63 <expand macro="advanced_optional_id_files" /> |
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64 <expand macro="input_qcov_hsp_perc" /> |
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65 </expand> |
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66 </inputs> |
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67 <outputs> |
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68 <data name="output1" format="tabular" label="${blast_type.value} $query.name vs @ON_DB_SUBJECT@"> |
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69 <expand macro="output_change_format" /> |
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70 </data> |
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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="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> |
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75 <param name="db_opts_selector" value="file" /> |
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76 <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> |
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77 <param name="database" value="" /> |
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78 <param name="evalue_cutoff" value="1e-40" /> |
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79 <param name="out_format" value="5" /> |
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80 <param name="adv_opts_selector" value="basic" /> |
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81 <output name="output1" file="blastn_rhodopsin_vs_three_human.xml" ftype="blastxml" /> |
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82 </test> |
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83 <test> |
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84 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> |
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85 <param name="db_opts_selector" value="file" /> |
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86 <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> |
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87 <param name="database" value="" /> |
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88 <param name="evalue_cutoff" value="1e-40" /> |
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89 <param name="out_format" value="6" /> |
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90 <param name="adv_opts_selector" value="basic" /> |
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91 <output name="output1" file="blastn_rhodopsin_vs_three_human.tabular" ftype="tabular" /> |
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92 </test> |
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93 <test> |
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94 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> |
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95 <param name="db_opts_selector" value="file" /> |
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96 <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> |
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97 <param name="database" value="" /> |
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98 <param name="evalue_cutoff" value="1e-40" /> |
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99 <param name="out_format" value="cols" /> |
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100 <param name="std_cols" value="qseqid,sseqid,pident" /> |
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101 <param name="ext_cols" value="qlen,slen" /> |
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102 <param name="adv_opts_selector" value="basic" /> |
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103 <output name="output1" file="blastn_rhodopsin_vs_three_human.columns.tabular" ftype="tabular" /> |
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104 </test> |
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105 <!-- Disable for ToolShed where *.loc tests not yet supported |
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106 See https://github.com/peterjc/galaxy_blast/issues/53 |
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107 <test> |
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108 <param name="query" value="chimera.fasta" ftype="fasta" /> |
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109 <param name="db_opts_selector" value="db" /> |
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110 <param name="database" value="three_human_mRNA" /> |
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111 <param name="out_format" value="6" /> |
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112 <param name="adv_opts_selector" value="advanced" /> |
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113 <param name="max_hits" value="1" /> |
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114 <output name="output1" file="blastn_chimera_vs_three_human_max1.tabular" ftype="tabular" /> |
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115 </test> |
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116 <test> |
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117 <param name="query" value="chimera.fasta" ftype="fasta" /> |
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118 <param name="db_opts_selector" value="db" /> |
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119 <param name="database" value="three_human_mRNA" /> |
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120 <param name="out_format" value="0" /> |
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121 <param name="adv_opts_selector" value="advanced" /> |
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122 <param name="max_hits" value="1" /> |
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123 <output name="output1" file="blastn_chimera_vs_three_human_max1.txt" ftype="txt" /> |
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124 </test> |
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125 --> |
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126 </tests> |
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127 <help> |
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128 |
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129 @SEARCH_TIME_WARNING@ |
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130 |
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131 **What it does** |
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132 |
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133 Search a *nucleotide database* using a *nucleotide query*, |
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134 using the NCBI BLAST+ blastn command line tool. |
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135 Algorithms include blastn, megablast, and discontiguous megablast. |
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136 |
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137 @FASTA_WARNING@ |
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138 |
3
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139 ----- |
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140 |
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141 @OUTPUT_FORMAT@ |
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142 |
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143 ------- |
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144 |
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145 **References** |
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146 |
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147 If you use this Galaxy tool in work leading to a scientific publication please |
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148 cite the following papers: |
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149 |
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150 @REFERENCES@ |
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151 </help> |
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152 <expand macro="blast_citations" /> |
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153 </tool> |