Mercurial > repos > devteam > ncbi_blast_plus

annotate tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @ 49:17f84d08f5a6 draft

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"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit f3980e76fb3b06f9c631e668f63f65055fc92cae-dirty"
author peterjc
date Tue, 08 Sep 2020 20:58:48 +0000
parents 00330a63ffcf
children 061c2abccfea
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17f84d08f5a6 "planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit f3980e76fb3b06f9c631e668f63f65055fc92cae-dirty"
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1 <tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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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>
6
856b73016ba1 v0.1.05 - Update citation information now GigaScience paper is out
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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 <![CDATA[
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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
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13 blastn
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14 @QUERY@
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15 @BLAST_DB_SUBJECT@
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16 -task '${blast_type}'
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17 -evalue '${evalue_cutoff}'
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18 @BLAST_OUTPUT@
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19 @THREADS@
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20 #if $adv_opts.adv_opts_selector=="advanced":
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21 ${adv_opts.strand}
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22 @ADV_FILTER_QUERY@
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23 @ADV_MAX_HITS@
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24 @ADV_WORD_SIZE@
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25 #if (str($adv_opts.identity_cutoff) and float(str($adv_opts.identity_cutoff)) > 0 ):
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26 -perc_identity '${adv_opts.identity_cutoff}'
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27 #end if
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28 ${adv_opts.ungapped}
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29 @ADV_ID_LIST_FILTER@
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30 @ADV_QCOV_HSP_PERC@
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31 ## only use window size if dc-megablast mode is used
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32 #if ($blast_type == "dc-megablast"):
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33 -window_size @ADV_WINDOW_SIZE@
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34 #end if
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35 @ADV_GAPOPEN@
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36 @ADV_GAPEXTEND@
0
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37 ## End of advanced options:
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38 #end if
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39 ]]>
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40 </command>
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41 <inputs>
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42 <expand macro="nucl_query" />
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43 <expand macro="input_conditional_nucleotide_db" />
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44 <param name="blast_type" argument="-task" type="select" display="radio" label="Type of BLAST">
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45 <option value="megablast">megablast - Traditional megablast used to find very similar (e.g., intraspecies or closely related species) sequences</option>
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46 <option value="blastn">blastn - Traditional BLASTN requiring an exact match of 11, for somewhat similar sequences</option>
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47 <option value="blastn-short">blastn-short - BLASTN program optimized for sequences shorter than 50 bases</option>
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48 <option value="dc-megablast">dc-megablast - Discontiguous megablast used to find more distant (e.g., interspecies) sequences</option>
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49 <!-- Using BLAST 2.2.24+ this gives an error:
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50 BLAST engine error: Program type 'vecscreen' not supported
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51 <option value="vecscreen">vecscreen</option>
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52 In any case, vecscreen has gone in BLAST+ 2.2.28
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53 -->
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54 <!-- BLAST+ 2.2.28 also offers rmblastn -->
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55 </param>
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56 <expand macro="input_evalue" />
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57 <expand macro="input_out_format" />
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58 <expand macro="advanced_options">
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59 <!-- Could use a select (yes, no, other) where other allows setting 'level window linker' -->
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60 <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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61 <expand macro="input_strand" />
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62 <expand macro="input_max_hits" />
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63 <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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64 <expand macro="input_word_size" />
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65 <param argument="-ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" />
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66 <expand macro="input_parse_deflines" />
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67 <expand macro="advanced_optional_id_files" />
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68 <expand macro="input_qcov_hsp_perc" />
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69 <!-- the help text here is unique to the blastx application, so macro not used -->
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70 <param name="window_size" type="integer" optional="true" min="0"
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71 label="Multiple hits window size: use 0 to specify 1-hit algorithm, leave blank for default"
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72 help="Only relevant for dc-megablast, and otherwise ignored. Default window size changes with substitution matrix and BLAST type.
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73 Entering a non-negative integer will override the default."/>
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74 <expand macro="input_gapopen"/>
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75 <expand macro="input_gapextend"/>
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76 </expand>
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77 </inputs>
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78 <outputs>
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79 <data name="output1" format="tabular" label="${blast_type.value} $query.name vs @ON_DB_SUBJECT@">
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80 <expand macro="output_change_format" />
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81 </data>
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82 </outputs>
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83 <tests>
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84 <test>
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85 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
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86 <param name="db_opts_selector" value="file" />
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87 <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" />
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88 <param name="database" value="" />
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89 <param name="evalue_cutoff" value="1e-40" />
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90 <param name="out_format" value="5" />
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91 <param name="adv_opts_selector" value="basic" />
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92 <output name="output1" file="blastn_rhodopsin_vs_three_human.xml" ftype="blastxml" />
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93 </test>
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94 <test>
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95 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
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96 <param name="db_opts_selector" value="file" />
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97 <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" />
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98 <param name="database" value="" />
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99 <param name="evalue_cutoff" value="1e-40" />
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100 <param name="out_format" value="6" />
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101 <param name="adv_opts_selector" value="basic" />
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102 <output name="output1" file="blastn_rhodopsin_vs_three_human.tabular" ftype="tabular" />
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103 </test>
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104 <test>
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105 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
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106 <param name="db_opts_selector" value="file" />
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107 <param name="subject" value="three_human_mRNA.fasta.gz" ftype="fasta.gz" />
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108 <param name="database" value="" />
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109 <param name="evalue_cutoff" value="1e-40" />
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110 <param name="out_format" value="6" />
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111 <param name="adv_opts_selector" value="basic" />
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112 <output name="output1" file="blastn_rhodopsin_vs_three_human.tabular" ftype="tabular" />
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113 </test>
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114 <test>
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115 <param name="query" value="rhodopsin_nucs.fasta" ftype="fasta" />
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116 <param name="db_opts_selector" value="file" />
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117 <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" />
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118 <param name="database" value="" />
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119 <param name="evalue_cutoff" value="1e-40" />
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120 <param name="out_format" value="cols" />
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121 <param name="std_cols" value="qseqid,sseqid,pident" />
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122 <param name="ext_cols" value="qlen,slen" />
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123 <param name="adv_opts_selector" value="basic" />
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124 <output name="output1" file="blastn_rhodopsin_vs_three_human.columns.tabular" ftype="tabular" />
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125 </test>
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126 <test>
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127 <param name="query" value="chimera.fasta" ftype="fasta" />
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128 <param name="db_opts_selector" value="db" />
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129 <param name="database" value="three_human_mRNA" />
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130 <param name="out_format" value="6" />
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131 <param name="adv_opts_selector" value="advanced" />
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132 <param name="max_hits" value="1" />
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133 <output name="output1" file="blastn_chimera_vs_three_human_max1.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="three_human_mRNA" />
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139 <param name="out_format" value="0" />
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140 <param name="adv_opts_selector" value="advanced" />
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141 <param name="max_hits" value="1" />
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142 <output name="output1" file="blastn_chimera_vs_three_human_max1.txt" ftype="txt" />
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143 </test>
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144 <test>
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145 <param name="query" value="chimera.fasta" ftype="fasta" />
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146 <param name="db_opts_selector" value="db" />
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147 <param name="database" value="three_human_mRNA" />
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148 <param name="out_format" value="6" />
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149 <output name="output1" file="blastn_chimera_vs_three_human_db.tabular" ftype="tabular" />
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150 </test>
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151 <test>
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152 <param name="query" value="chimera.fasta" ftype="fasta" />
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153 <param name="db_opts_selector" value="db" />
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154 <param name="database" value="rhodopsin_nucs" />
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155 <param name="out_format" value="6" />
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156 <output name="output1" file="blastn_chimera_vs_rhodopsin_db.tabular" ftype="tabular" />
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157 </test>
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158 <test>
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159 <param name="query" value="chimera.fasta" ftype="fasta" />
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160 <param name="db_opts_selector" value="db" />
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161 <param name="database" value="rhodopsin_nucs" />
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162 <param name="out_format" value="6" />
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163 <param name="adv_opts_selector" value="advanced" />
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164 <param name="max_hsps" value="1" />
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165 <output name="output1" file="blastn_chimera_vs_rhodopsin_db_max_hsps1.tabular" ftype="tabular" />
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166 </test>
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167 <!-- next test is passing in two blast databases -->
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168 <test>
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169 <param name="query" value="chimera.fasta" ftype="fasta" />
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170 <param name="db_opts_selector" value="db" />
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171 <param name="database" value="three_human_mRNA,rhodopsin_nucs" />
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172 <param name="out_format" value="6" />
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173 <output name="output1" file="blastn_chimera_vs_three_human_and_rhodopsin_db.tabular" ftype="tabular" />
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174 </test>
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175 </tests>
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176 <help>
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177
0
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178 @SEARCH_TIME_WARNING@
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179
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180 **What it does**
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181
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182 Search a *nucleotide database* using a *nucleotide query*,
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183 using the NCBI BLAST+ blastn command line tool.
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184 Algorithms include blastn, megablast, and discontiguous megablast.
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185
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186 @FASTA_WARNING@
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187
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188 -----
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189
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190 @OUTPUT_FORMAT@
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191
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192 -------
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193
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194 @CLI_OPTIONS@
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195
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196 -------
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197
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198 **References**
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199
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200 If you use this Galaxy tool in work leading to a scientific publication please
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201 cite the following papers:
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202
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203 @REFERENCES@
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204 </help>
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205 <expand macro="blast_citations" />
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206 </tool>