Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @ 22:6f386c5dc4fb draft
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
author | peterjc |
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date | Mon, 18 Sep 2017 06:21:27 -0400 |
parents | 3034ce97dd33 |
children | 31e517610e1f |
rev | line source |
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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 detect_errors="aggressive"> |
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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 argument="-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" argument="-task" 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" argument="-dust" 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" argument="-perc_identity" type="float" min="0" max="100" value="0" label="Percent identity cutoff" 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 argument="-word_size" type="integer" min="0" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4" /> |
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59 <param argument="-ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /> |
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60 <expand macro="input_parse_deflines" /> |
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61 <expand macro="advanced_optional_id_files" /> |
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62 <expand macro="input_qcov_hsp_perc" /> |
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63 </expand> |
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64 </inputs> |
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65 <outputs> |
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66 <data name="output1" format="tabular" label="${blast_type.value} $query.name vs @ON_DB_SUBJECT@"> |
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67 <expand macro="output_change_format" /> |
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68 </data> |
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69 </outputs> |
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70 <tests> |
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71 <test> |
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72 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> |
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73 <param name="db_opts_selector" value="file" /> |
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74 <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> |
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75 <param name="database" value="" /> |
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76 <param name="evalue_cutoff" value="1e-40" /> |
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77 <param name="out_format" value="5" /> |
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78 <param name="adv_opts_selector" value="basic" /> |
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79 <output name="output1" file="blastn_rhodopsin_vs_three_human.xml" ftype="blastxml" /> |
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80 </test> |
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81 <test> |
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82 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> |
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83 <param name="db_opts_selector" value="file" /> |
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84 <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> |
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85 <param name="database" value="" /> |
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86 <param name="evalue_cutoff" value="1e-40" /> |
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87 <param name="out_format" value="6" /> |
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88 <param name="adv_opts_selector" value="basic" /> |
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89 <output name="output1" file="blastn_rhodopsin_vs_three_human.tabular" ftype="tabular" /> |
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90 </test> |
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91 <test> |
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92 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" /> |
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93 <param name="db_opts_selector" value="file" /> |
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94 <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> |
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95 <param name="database" value="" /> |
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96 <param name="evalue_cutoff" value="1e-40" /> |
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97 <param name="out_format" value="cols" /> |
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98 <param name="std_cols" value="qseqid,sseqid,pident" /> |
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99 <param name="ext_cols" value="qlen,slen" /> |
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100 <param name="adv_opts_selector" value="basic" /> |
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101 <output name="output1" file="blastn_rhodopsin_vs_three_human.columns.tabular" ftype="tabular" /> |
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102 </test> |
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103 <test> |
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104 <param name="query" value="chimera.fasta" ftype="fasta" /> |
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105 <param name="db_opts_selector" value="db" /> |
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106 <param name="database" value="three_human_mRNA" /> |
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107 <param name="out_format" value="6" /> |
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108 <param name="adv_opts_selector" value="advanced" /> |
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109 <param name="max_hits" value="1" /> |
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110 <output name="output1" file="blastn_chimera_vs_three_human_max1.tabular" ftype="tabular" /> |
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111 </test> |
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112 <test> |
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113 <param name="query" value="chimera.fasta" ftype="fasta" /> |
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114 <param name="db_opts_selector" value="db" /> |
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115 <param name="database" value="three_human_mRNA" /> |
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116 <param name="out_format" value="0" /> |
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117 <param name="adv_opts_selector" value="advanced" /> |
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118 <param name="max_hits" value="1" /> |
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119 <output name="output1" file="blastn_chimera_vs_three_human_max1.txt" ftype="txt" /> |
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120 </test> |
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121 <test> |
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122 <param name="query" value="chimera.fasta" ftype="fasta" /> |
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123 <param name="db_opts_selector" value="db" /> |
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124 <param name="database" value="three_human_mRNA" /> |
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125 <param name="out_format" value="6" /> |
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126 <output name="output1" file="blastn_chimera_vs_three_human_db.tabular" ftype="tabular" /> |
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127 </test> |
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128 <test> |
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129 <param name="query" value="chimera.fasta" ftype="fasta" /> |
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130 <param name="db_opts_selector" value="db" /> |
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131 <param name="database" value="rhodopsin_nucs" /> |
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132 <param name="out_format" value="6" /> |
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133 <output name="output1" file="blastn_chimera_vs_rhodopsin_db.tabular" ftype="tabular" /> |
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134 </test> |
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135 <test> |
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136 <param name="query" value="chimera.fasta" ftype="fasta" /> |
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137 <param name="db_opts_selector" value="db" /> |
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138 <param name="database" value="rhodopsin_nucs" /> |
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139 <param name="out_format" value="6" /> |
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140 <param name="adv_opts_selector" value="advanced" /> |
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141 <param name="max_hsps" value="1" /> |
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142 <output name="output1" file="blastn_chimera_vs_rhodopsin_db_max_hsps1.tabular" ftype="tabular" /> |
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143 </test> |
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144 <!-- next test is passing in two blast databases --> |
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145 <test> |
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146 <param name="query" value="chimera.fasta" ftype="fasta" /> |
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147 <param name="db_opts_selector" value="db" /> |
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148 <param name="database" value="three_human_mRNA,rhodopsin_nucs" /> |
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149 <param name="out_format" value="6" /> |
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150 <output name="output1" file="blastn_chimera_vs_three_human_and_rhodopsin_db.tabular" ftype="tabular" /> |
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151 </test> |
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152 </tests> |
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153 <help> |
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154 |
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155 @SEARCH_TIME_WARNING@ |
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156 |
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157 **What it does** |
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158 |
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159 Search a *nucleotide database* using a *nucleotide query*, |
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160 using the NCBI BLAST+ blastn command line tool. |
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161 Algorithms include blastn, megablast, and discontiguous megablast. |
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162 |
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163 @FASTA_WARNING@ |
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164 |
3
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165 ----- |
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166 |
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167 @OUTPUT_FORMAT@ |
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168 |
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169 ------- |
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170 |
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171 **References** |
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172 |
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173 If you use this Galaxy tool in work leading to a scientific publication please |
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174 cite the following papers: |
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175 |
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176 @REFERENCES@ |
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177 </help> |
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178 <expand macro="blast_citations" /> |
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179 </tool> |