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annotate diamond.xml @ 1:df7738595640 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
author bgruening
date Mon, 06 Feb 2017 07:08:25 -0500
parents 98037ef3d2a9
children 830516f9521b
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df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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1 <tool id="bg_diamond" name="Diamond" version="@VERSION@">
0
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2 <description>alignment tool for short sequences against a protein database</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <expand macro="version_command" />
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9 <command>
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10 <![CDATA[
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11
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12 #if $ref_db_source.db_source == "history":
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13 ln -s $ref_db_source.reference_database ./database.dmnd
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14 #else:
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15 ln -s ${ref_db_source.index.fields.db_path} ./database.dmnd
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16 #end if
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17
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18 &&
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19
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20 diamond
1
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21 $method_select
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22 --threads "\${GALAXY_SLOTS:-12}"
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23 --db ./database
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24 --query '$query'
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25 --query-gencode '$query_gencode'
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27 #if $output.outfmt == "5"
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28 --outfmt '5'
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29 --out '$blast_xml'
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30 $output.salltitles
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31 #else if $output.outfmt == "6"
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32 --outfmt '6' #echo ' '.join(str($output.fields).split(','))
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33 --out '$blast_tabular'
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34 #else if $output.outfmt == "101"
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35 --outfmt '101'
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36 --out '$sam_output'
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37 $output.salltitles
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38 #end if
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39
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40 --compress '0'
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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41 $sensitive
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42 $more_sensitive
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43 --gapopen '$gapopen'
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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44 --gapextend '$gapextend'
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45 --matrix '$matrix'
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46 --seg '$seg'
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47
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48 #if str($hit_filter.hit_filter_select) == 'max':
1
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49 --max-target-seqs '$hit_filter.max_target_seqs'
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50 #else:
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51 --top '$hit_filter.top'
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52 #end if
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53
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54 #if str($filter_score.filter_score_select) == 'evalue':
1
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55 --evalue '$filter_score.evalue'
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56 #else:
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57 --min-score '$filter_score.min_score'
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58 #end if
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59
1
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60 --id '$id'
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61 --query-cover '$query_cover'
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62 --block-size '$block_size'
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63 ]]>
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64 </command>
1
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65
0
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66 <inputs>
1
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67 <param name="method_select" type="select" label="What do you want to align?" help="(--blastp/--blastx)">
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68 <option value="blastp">Align amino acid query sequences (blastp)</option>
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69 <option value="blastx">Align DNA query sequences (blastx)</option>
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70 </param>
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71 <param argument="--query" type="data" format="fasta,fastq" label="Input query file in FASTA or FASTQ format" />
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72 <conditional name="ref_db_source">
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73 <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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74 <option value="indexed">Use a built-in index</option>
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75 <option value="history">Use one from the history</option>
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76 </param>
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77 <when value="indexed">
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78 <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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79 <options from_data_table="diamond_database">
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80 <filter type="sort_by" column="2"/>
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81 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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82 </options>
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83 </param>
1
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84 </when>
0
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85 <when value="history">
1
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86 <param name="reference_database" type="data" format="dmnd" label="Select the reference database" />
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87 </when>
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88 </conditional>
1
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89 <param name="query_gencode" argument="--query-gencode" type="select" label="Genetic code used for translation of query in BLASTX mode" help="">
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90 <option value="1">The Standard Code</option>
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91 <option value="2">The Vertebrate Mitochondrial Code</option>
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92 <option value="3">The Yeast Mitochondrial Code</option>
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93 <option value="4">The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
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94 <option value="5">The Invertebrate Mitochondrial Code</option>
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95 <option value="6">The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
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96 <option value="9">The Echinoderm and Flatworm Mitochondrial Code</option>
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97 <option value="10">The Euplotid Nuclear Code</option>
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98 <option value="11">The Bacterial, Archaeal and Plant Plastid Code</option>
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99 <option value="12">The Alternative Yeast Nuclear Code</option>
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100 <option value="13">The Ascidian Mitochondrial Code</option>
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101 <option value="14">The Alternative Flatworm Mitochondrial Code</option>
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102 <option value="16">Chlorophycean Mitochondrial Code</option>
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103 <option value="21">Trematode Mitochondrial Code</option>
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104 <option value="22">Scenedesmus obliquus Mitochondrial Code</option>
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105 <option value="23">Thraustochytrium Mitochondrial Code</option>
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106 <option value="24">Pterobranchia Mitochondrial Code</option>
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107 <option value="5">Candidate Division SR1 and Gracilibacteria Code</option>
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108 <option value="26">Pachysolen tannophilus Nuclear Code</option>
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109 </param>
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110 <conditional name="output">
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111 <param argument="--outfmt" type="select" label="Format of output file " help="">
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112 <option value="5">BLAST XML</option>
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113 <option value="6">BLAST tabular</option>
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114 <option value="101">SAM</option>
0
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115 </param>
1
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116 <when value="5">
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117 <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full length subject titles in output?" help=""/>
0
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118 </when>
1
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119 <when value="6">
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120 <param name="fields" type="select" label="Tabular fields" help="" multiple="true">
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121 <option value="qseqid" selected="true">Query Seq - id</option>
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122 <option value="sseqid" selected="true">Subject Seq - id</option>
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123 <option value="sallseqid">All subject Seq - id(s)</option>
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124 <option value="qlen">Query sequence length</option>
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125 <option value="slen">Subject sequence length</option>
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126 <option value="pident" selected="true">Percentage of identical matches</option>
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127 <option value="length" selected="true">Alignment length</option>
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128 <option value="nident">Number of identical matches</option>
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129 <option value="mismatch" selected="true">Number of mismatches</option>
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130 <option value="positive">Number of positive - scoring matches</option>
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131 <option value="gapopen" selected="true">Number of gap openings</option>
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132 <option value="gaps">Total number of gaps</option>
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133 <option value="ppos">Percentage of positive - scoring matches</option>
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134 <option value="qstart" selected="true">Start of alignment in query</option>
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135 <option value="qend" selected="true">End of alignment in query</option>
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136 <option value="sstart" selected="true">Start of alignment in subject</option>
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137 <option value="send" selected="true">End of alignment in subject</option>
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138 <option value="qseq">Aligned part of query sequence</option>
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139 <option value="sseq">Aligned part of subject sequence</option>
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140 <option value="evalue" selected="true">Expect value</option>
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141 <option value="bitscore" selected="true">Bit score</option>
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142 <option value="score">Raw score</option>
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143 <option value="qframe">Query frame</option>
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144 <option value="stitle">Subject Title</option>
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145 <option value="salltitles">All Subject Title(s)</option>
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146 <option value="qcovhsp">Query Coverage Per HSP</option>
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147 </param>
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148 </when>
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149 <when value="101">
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150 <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full length subject titles in output?" help=""/>
0
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151 </when>
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152 </conditional>
1
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153 <param argument="--sensitive" type="boolean" truevalue="--sensitive" falsevalue="" checked="false" label="Trigger the sensitive alignment mode with a 16x9 seed shape configuration?" help=""/>
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154 <param name="more_sensitive" argument="--more-sensitive" type="boolean" truevalue="--more-sensitive" falsevalue="" checked="false" label="Trigger the more sensitive mode?" help="This mode provides some additional sensitivity compared to the sensitive mode."/>
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155 <param argument="--gapopen" type="integer" value="11" label="Gap open penalty" help="" />
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156 <param argument="--gapextend" type="integer" value="1" label="Gap extension penalty" help="" />
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157 <param argument="--matrix" type="select" label="Scoring matrix" help="In brackets are the supported values for (gap open)/(gap extend)">
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158 <option value="BLOSUM45">BLOSUM45 ((10-13)/3; (12-16)/2; (16-19)/1)</option>
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159 <option value="BLOSUM50">BLOSUM50 ((9-13)/3; (12-16)/2; (15-19)/1)</option>
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160 <option value="BLOSUM62" selected="True">BLOSUM62 ((6-11)/2; (9-13)/1)</option>
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161 <option value="BLOSUM80">BLOSUM80 ((6-9)/2; 13/2; 25/2; (9-11)/1)</option>
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162 <option value="BLOSUM90">BLOSUM90 ((6-9)/2; (9-11)/1)</option>
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163 <option value="PAM250">PAM250 ((11-15)/3; (13-17)/2; (17-21)/1)</option>
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164 <option value="PAM70">PAM70 ((6-8)/2; (9-11)/1)</option>
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165 <option value="PAM30">PAM30 ((5-7)/2; (8-10)/1)</option>
0
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166 </param>
1
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167 <param argument="--seg" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Enable SEG masking of low complexity segments in the query?" help=""/>
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168 <conditional name="hit_filter">
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169 <param name="hit_filter_select" type="select" label="Method to restrict the number of hits?">
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170 <option value="max">Maximum number of target sequences</option>
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171 <option value="top">Percentage of top alignment score</option>
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172 </param>
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173 <when value="max">
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174 <param name="max_target_seqs" argument="--max-target-seqs" type="integer" value="25" label="The maximum number of target sequences per query to keep alignments for" help="" />
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175 </when>
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176 <when value="top">
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177 <param argument="--top" type="integer" value="0" label="Keep alignments within the given percentage range of the top alignment score for a quer" help="" />
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178 </when>
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179 </conditional>
0
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180 <conditional name="filter_score">
1
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181 <param name="filter_score_select" type="select" label="Method to filter?" help="(--evalue/--min-score)">
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98037ef3d2a9 Imported from capsule None
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182 <option value="evalue">Maximum e-value to report alignments</option>
1
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183 <option value="min-score">Minimum bit score to report alignments</option>
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184 </param>
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185 <when value="evalue">
1
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186 <param argument="--evalue" type="float" value="0.001" label="Maximum expected value to keep an alignment" />
0
98037ef3d2a9 Imported from capsule None
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187 </when>
1
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188 <when value="min-score">
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189 <param name="min_score" argument="--min-score" type="integer" value="0" label="Minimum bit score to keep an alignment" help="(--min-score)" />
0
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190 </when>
98037ef3d2a9 Imported from capsule None
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191 </conditional>
1
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192 <param argument="--id" type="integer" value="0" label="Minimum identity percentage to report an alignment" help="" />
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193 <param name="query_cover" argument="--query-cover" type="integer" value="0" label="Minimum query cover percentage to report an alignment" help="" />
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194 <param name="block_size" argument="--block-size" type="float" value="2" label="Block size in billions of sequence letters to be processed at a time" help="" />
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195 </inputs>
0
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196
98037ef3d2a9 Imported from capsule None
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197 <outputs>
1
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198 <data format="xml" name="blast_xml" label="${tool.name} on ${on_string}">
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199 <filter>output["outfmt"] == "5"</filter>
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200 </data>
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201 <data format="tabular" name="blast_tabular" label="${tool.name} on ${on_string}">
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202 <filter>output["outfmt"] == "6"</filter>
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203 </data>
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204 <data format="sam" name="sam_output" label="${tool.name} on ${on_string}">
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205 <filter>output["outfmt"] == "101"</filter>
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206 </data>
0
98037ef3d2a9 Imported from capsule None
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207 </outputs>
1
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208
0
98037ef3d2a9 Imported from capsule None
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209 <tests>
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210 <test>
1
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211 <param name="method_select" value="blastp" />
0
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212 <param name="query" value="protein.fasta" ftype="fasta"/>
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213 <param name="db_source" value="history"/>
1
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214 <param name="reference_database" value="db.dmnd"/>
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215 <param name="query_gencode" value="1"/>
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216 <param name="outfmt" value="6"/>
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217 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
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218 <param name="sensitive" value=""/>
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219 <param name="more_sensitive" value=""/>
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220 <param name="gapopen" value="11"/>
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221 <param name="gapextend" value="1"/>
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222 <param name="matrix" value="BLOSUM62"/>
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223 <param name="seg" value="yes"/>
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224 <param name="hit_filter_select" value="max"/>
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225 <param name="max_target_seqs" value="25" />
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226 <param name="filter_score_select" value="evalue"/>
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227 <param name="evalue" value="0.001" />
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228 <param name="id" value="0"/>
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229 <param name="query_cover" value="0"/>
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230 <param name="block_size" value="2"/>
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231 <output name="blast_tabular" file="diamond_results.tabular"/>
0
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232 </test>
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233 </tests>
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234
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235 <help>
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236 <![CDATA[
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237
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238 **What it does**
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239
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240 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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241 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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242 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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243 times faster than BLASTX, finding more than 94% of all matches.
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244
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245 The DIAMOND algorithm is designed for the alignment of large datasets. The algorithm is not efficient for a small number of query sequences or only a single one of them, and speed will be low. BLAST is recommend for small datasets.
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246
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247 .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/
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248
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249 **Input**
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250
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251 Input data is a large protein or nucleotide sequence file.
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252
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253
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254 **Output**
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255
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256 Diamond gives you a tabular output file with 12 columns:
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257
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258 Column Description
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259 1 Query Seq-id (ID of your sequence)
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260 2 Subject Seq-id (ID of the database hit)
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261 3 Percentage of identical matches
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262 4 Alignment length
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263 5 Number of mismatches
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264 6 Number of gap openings
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265 7 Start of alignment in query
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266 8 End of alignment in query
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267 9 Start of alignment in subject (database hit)
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268 10 End of alignment in subject (database hit)
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269 11 Expectation value (E-value)
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270 12 Bit score
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271
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272
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273 Supported values for gap open and gap extend parameters depending on the selected scoring matrix.
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274
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275 ======== ============================================
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276 Matrix Supported values for (gap open)/(gap extend)
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277 ======== ============================================
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278 BLOSUM45 (10-13)/3; (12-16)/2; (16-19)/1
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279 BLOSUM50 (9-13)/3; (12-16)/2; (15-19)/1
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280 BLOSUM62 (6-11)/2; (9-13)/1
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281 BLOSUM80 (6-9)/2; 13/2; 25/2; (9-11)/1
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282 BLOSUM90 (6-9)/2; (9-11)/1
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283 PAM250 (11-15)/3; (13-17)/2; (17-21)/1
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284 PAM70 (6-8)/2; (9-11)/1
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285 PAM30 (5-7)/2; (8-10)/1
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286 ======== ============================================
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287
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288
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289 ]]>
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290 </help>
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291 <expand macro="citations" />
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292 </tool>