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1 <tool id="bg_diamond" name="Diamond" version="0.1.6.0">
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2 <description>alignment tool for short sequences against a protein database</description>
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3 <requirements>
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4 <requirement type="package" version="0.6.13">diamond</requirement>
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5 </requirements>
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6 <command>
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7 <![CDATA[
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8
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9 #if $ref_db_source.db_source == "history":
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10 ln -s $ref_db_source.reference_database ./database.dmnd
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11 #else:
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12 ln -s ${ref_db_source.index.fields.db_path} ./database.dmnd
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13 #end if
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14
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15 &&
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16
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17 diamond
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18 $method.method_select
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19 --threads "\${GALAXY_SLOTS:-12}"
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20 --db ./database
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21 --query $query
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22 --out $blast_output
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23 ##--sam $sam_output
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24 --compress 0
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25 --tmpdir ./
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26
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27 #if str($hit_filter.hit_filter_select) == 'max':
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28 --max-target-seqs $hit_filter.max
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29 #else:
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30 --top $hit_filter.percentage
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31 #end if
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32
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33 #if str($filter_score.filter_score_select) == 'evalue':
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34 --evalue $filter_score.evalue
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35 #else:
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36 --evalue $filter_score.bitscore
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37 #end if
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38
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39 --id $identity
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40 $sensitive
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41 --gapopen $method.gapopen
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42 --gapextend $method.gapextend
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43 --matrix $matrix
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44 $seg
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45 $salltitles
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46
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47 ]]>
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48 </command>
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49 <inputs>
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50
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51 <param name="query" type="data" format="fasta" label="Input query file in FASTA format" />
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52
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53 <conditional name="ref_db_source">
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54 <param name="db_source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
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55 <option value="indexed">Use a built-in index</option>
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56 <option value="history">Use one from the history</option>
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57 </param>
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58 <when value="indexed">
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59 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin">
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1
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60 <options from_data_table="diamond_database">
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0
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61 <column name="value" index="0"/>
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62 <column name="name" index="2"/>
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63 <column name="db_path" index="3"/>
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64 <filter type="sort_by" column="2"/>
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65 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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66 </options>
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67 </param>
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68 </when> <!-- build-in -->
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69 <when value="history">
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4
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70 <param name="reference_database" type="data" format="diamond_database" label="Select the reference database" />
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0
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71 </when> <!-- history -->
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72 </conditional>
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73
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2
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74 <conditional name="method">
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75 <param name="method_select" type="select" label="What do you want to align" help="(--blastp/--blastx)">
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76 <option value="blastp">Align amino acid query sequences (blastp)</option>
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77 <option value="blastx">Align DNA query sequences (blastx)</option>
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78 </param>
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79 <when value="blastp">
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80 <param name="gapopen" type="integer" value="11" label="Gap open panalty" help="(--gapopen)" />
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81 <param name="gapextend" type="integer" value="1" label="Gap extend panalty" help="(--gapextend)" />
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82 </when>
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83 <when value="blastx">
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84 <param name="gapopen" type="integer" value="-1" label="Gap open panalty" help="(--gapopen)" />
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85 <param name="gapextend" type="integer" value="-1" label="Gap extend panalty" help="(--gapextend)" />
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86 </when>
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87 </conditional>
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88
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0
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89 <param name="matrix" type="select" label="Select scoring matrix" help="(--matrix)">
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90 <option value="BLOSUM45">BLOSUM45</option>
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91 <option value="BLOSUM50">BLOSUM50</option>
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92 <option value="BLOSUM62" selected="True">BLOSUM62</option>
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93 <option value="BLOSUM80">BLOSUM80</option>
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94 <option value="BLOSUM90">BLOSUM90</option>
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95 <option value="PAM250">PAM250</option>
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96 <option value="PAM70">PAM70</option>
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97 <option value="PAM30">PAM30</option>
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98 </param>
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99
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100 <conditional name="filter_score">
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101 <param name="filter_score_select" type="select" label="Filter by score" help="(--evalue/--min-score)">
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102 <option value="evalue">Maximum e-value to report alignments</option>
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103 <option value="bit">Minimum bit score to report alignments</option>
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104 </param>
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105 <when value="evalue">
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106 <param name="evalue" type="float" value="0.001" label="Filter by evalue" help="(--evalue)" />
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107 </when>
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108 <when value="bit">
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109 <param name="bitscore" type="integer" value="0" label="Filter by bit score" help="(--min-score)" />
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110 </when>
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111 </conditional>
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112
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113 <conditional name="hit_filter">
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114 <param name="hit_filter_select" type="select" label="Restrict number of hits by" help="(--max-target-seqs/--top)">
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115 <option value="max">Maximum number of target sequences</option>
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116 <option value="percentage">Percentage of top alignment score</option>
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117 </param>
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118 <when value="max">
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119 <param name="max" type="integer" value="25" label="How many hits?" help="(--max-target-seqs)" />
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120 </when>
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121 <when value="percentage">
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122 <param name="percentage" type="integer" value="0" label="How many percentage" help="(--top)" />
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123 </when>
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124 </conditional>
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125
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126 <param name="identity" type="integer" value="0" label="minimum identity to report an alignment" help="in percentage (--id)" />
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127 <param name="salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="false"
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128 label="Print subject titles into the blast tabular format" help="(--salltitles)"/>
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129 <param name="seg" type="boolean" truevalue="--seg yes" falsevalue="--seg no" checked="true"
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130 label="Enable SEG masking of queries" help="(--seg)"/>
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131 <param name="sensitive" type="boolean" truevalue="--sensitive" falsevalue="" checked="false"
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132 label="Enable sensitive mode" help="(--sensitive)"/>
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133 </inputs>
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134 <outputs>
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135 <!--data format="sam" name="sam_output"/-->
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136 <data format="tabular" name="blast_output"/>
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137 </outputs>
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138 <tests>
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139 <test>
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140 <param name="method" value="blastp"/>
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141 <param name="query" value="protein.fasta" ftype="fasta"/>
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4
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142 <param name="reference_database" value="diamond_makedb_result1.dmnd" ftype="diamond_database"/>
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0
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143 <param name="db_source" value="history"/>
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144 <output name="blast_output" file="diamond_result1.tabular" ftpye="tabular"/>
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145 </test>
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146 </tests>
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147 <help>
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148 <![CDATA[
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149
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150 .. class:: infomark
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151
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152 **What it does**
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153
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154 DIAMOND_ is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.
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155 On Illumina reads of length 100-150bp, in fast mode, DIAMOND is about 20,000 times faster than BLASTX, while reporting
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156 about 80-90% of all matches that BLASTX finds, with an e-value of at most 1e-5. In sensitive mode, DIAMOND ist about 2,500
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157 times faster than BLASTX, finding more than 94% of all matches.
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158
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159 .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/
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160
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161
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162 Supported values for gap open and gap extend parameters depending on the selected scoring matrix.
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163
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164 ======== ============================================
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165 Matrix Supported values for (gap open)/(gap extend)
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166 ======== ============================================
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167 BLOSUM45 (10-13)/3; (12-16)/2; (16-19)/1
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168 BLOSUM50 (9-13)/3; (12-16)/2; (15-19)/1
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169 BLOSUM62 (6-11)/2; (9-13)/1
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170 BLOSUM80 (6-9)/2; 13/2; 25/2; (9-11)/1
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171 BLOSUM90 (6-9)/2; (9-11)/1
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172 PAM250 (11-15)/3; (13-17)/2; (17-21)/1
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173 PAM70 (6-8)/2; (9-11)/1
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174 PAM30 (5-7)/2; (8-10)/1
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175 ======== ============================================
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176
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177
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178 ]]>
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179 </help>
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180 <citations>
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181 <citation type="doi">10.1038/nmeth.3176</citation>
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182 </citations>
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183 </tool>
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