Mercurial > repos > iuc > vsearch

annotate vsearch_macros.xml @ 10:32e8ed5c6100 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 98411bbc8c371cf56d81fc4a1402ee64efef41eb"
author iuc
date Wed, 04 Nov 2020 07:35:42 +0000
parents d918f0219e81
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
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1 <macros>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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2 <xml name="requirements">
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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3 <requirements>
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4 <requirement type="package" version="@VERSION@">vsearch</requirement>
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5 </requirements>
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6 </xml>
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7 <token name="@VERSION@">2.8.3</token>
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8
0
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9 <xml name="version_command">
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10 <version_command>vsearch --version | head -n 1 | awk '{print $2}' | sed 's/,//'</version_command>
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11 </xml>
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12 <xml name="stdio">
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13 <stdio>
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14 <exit_code range="1:" />
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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15 <exit_code range=":-1" />
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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16 <regex match="Error:" />
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17 <regex match="Exception:" />
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18 </stdio>
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19 </xml>
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20
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21 <xml name="topn">
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22 <param name="topn" type="integer" value="" optional="True" label="Output just first n sequences"
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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23 help="(--topn)"/>
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24 </xml>
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25
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26 <xml name="maxaccepts">
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27 <param name="maxaccepts" type="integer" value="1" label="Number of hits to accept and show per strand"
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28 help="(--maxaccepts)"/>
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29 </xml>
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30 <xml name="maxrejects">
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31 <param name="maxrejects" type="integer" value="32" label="Number of non-matching hits to consider"
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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32 help="(--maxrejects)"/>
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33 </xml>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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34 <xml name="qmask">
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35 <param name="qmask" type="select" label="Mask sequences" help="(--qmask)">
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36 <option value="none">No masking</option>
0
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37 <option value="dust" selected="True">dust</option>
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38 <option value="soft">soft</option>
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39 </param>
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40 </xml>
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41
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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42 <xml name="hardmask">
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43 <param name="hardmask" type="boolean" truevalue="--hardmask" falsevalue="" checked="False"
0
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44 label="Mask by replacing with N instead of lower case" help="(--hardmask)"/>
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45 </xml>
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46
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47 <xml name="id_and_iddef">
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48 <param name="iddef" type="select" label="ID definition" help="(--iddef)">
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49 <option value="0">CD-HIT</option>
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50 <option value="1">all</option>
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51 <option value="2" selected="True">int</option>
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52 <option value="3">MBL</option>
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53 <option value="4">BLAST</option>
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54 </param>
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55 <param name="id" type="float" value="" optional="True" label="Reject hit if identity is lower than this value"
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56 help="(--id)"/>
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57 </xml>
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58
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59 <xml name="self_and_selfid">
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60 <param name="self_param" type="boolean" truevalue="--self" falsevalue="" checked="False"
0
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61 label="Exclude identical labels for --uchime_ref" help="(--self)"/>
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62 <param name="selfid_param" type="boolean" truevalue="--selfid" falsevalue="" checked="False"
0
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63 label="Exclude identical sequences for --uchime_ref" help="(--selfid)"/>
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64 </xml>
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65
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66 <xml name="strand">
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67 <param name="strand" type="select" label="Strand specific clustering" help="(--strand)">
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68 <option value="plus" selected="True">Plus strand</option>
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69 <option value="both">Both strands</option>
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70 </param>
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71 </xml>
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73 <xml name="sizein">
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74 <param name="sizein" type="boolean" truevalue="--sizein" falsevalue="" checked="False"
0
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75 label="Read abundance annotation from input" help="(--sizein)"/>
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76 </xml>
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78 <xml name="sizeout">
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79 <param name="sizeout" type="boolean" truevalue="--sizeout" falsevalue="" checked="False"
0
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80 label="Write cluster abundances to centroid file" help="(--sizeout)"/>
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81 </xml>
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83 <xml name="uclust_like_output">
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84 <param name="uc" type="boolean" truevalue="--uc" falsevalue="" checked="False"
0
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85 label="UCLUST-like output" help="(--uc)"/>
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86 </xml>
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88 <token name="@GENERAL@">
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89 --threads "\${GALAXY_SLOTS:-4}"
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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90 --notrunclabels
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91 </token>
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iuc
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92 <token name="@USERFIELDS@">
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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93 #if $userfields_output.userfields_output_select == 'yes':
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94 --userfields '#echo '+'.join( str($userfields_output.userfields).split(',') )#'
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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95 --userout $userout
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96 #end if
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97 </token>
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98 <xml name="userfields_output">
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99 <data name="userout" format="tabular" label="${tool.name} on ${on_string}: tabular output">
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100 <filter>userfields_output.userfields_output_select == 'yes'</filter>
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101 </data>
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102 </xml>
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103
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104 <xml name="userfields">
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105 <conditional name="userfields_output">
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106 <param name="userfields_output_select" type="select" label="User defined tabular output" help="(--userfields)">
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107 <option value="yes">Yes</option>
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108 <option value="no" selected="True">No</option>
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109 </param>
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110 <when value="yes">
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111 <param name="userfields" type="select" multiple="True" label="Fields in tabular output" help="For more information about the columns please scroll down to the tool help. (--userfields)">
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112 <option value="aln">Print a string of M (match), D (delete, i.e. a gap in the query) and I (insert, i.e. a gap in the target) representing the pairwise alignment</option>
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113 <option value="alnlen">Print the length of the query-target alignment (number of columns)</option>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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114 <option value="bits">Bit score (not computed for nucleotide alignments)</option>
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115 <option value="caln">Compact representation of the pairwise alignment using the CIGAR format (Compact Idiosyncratic Gapped Alignment Report): M (match), D (deletion) and I (insertion)</option>
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116 <option value="evalue" selected="True">E-value (not computed for nucleotide alignments)</option>
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117 <option value="exts">Number of columns containing a gap extension (zero or positive integer value)</option>
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118 <option value="gaps">Number of columns containing a gap (zero or positive integer value)</option>
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119 <option value="id">Percentage of identity</option>
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120 <option value="id0">CD-HIT definition of the percentage of identity</option>
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121 <option value="id1">The percentage of identity</option>
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122 <option value="id2">The percentage of identity</option>
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123 <option value="id3">Marine Biological Lab definition of the percentage of identity</option>
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124 <option value="id4">BLAST definition of the percentage of identity</option>
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125 <option value="ids">Number of matches in the alignment</option>
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126 <option value="mism">Number of mismatches in the alignment</option>
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127 <option value="opens">Number of columns containing a gap opening</option>
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128 <option value="pairs">Number of columns containing only nucleotides</option>
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129 <option value="pctgaps">Number of columns containing gaps expressed as a percentage of the alignment length</option>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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130 <option value="pctpv">Percentage of positive columns. When working with nucleotide sequences, this is equivalent to the percentage of matches</option>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
iuc
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131 <option value="pv">Number of positive columns. When working with nucleotide sequences, this is equivalent to the number of matches</option>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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132 <option value="qcov">Fraction of the query sequence that is aligned with the target sequence</option>
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133 <option value="qframe">Query frame (-3 to +3). That field only concerns coding sequences and is not computed by vsearch</option>
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134 <option value="qhi">Last nucleotide of the query aligned with the target</option>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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135 <option value="qihi">Last nucleotide of the query aligned with the target</option>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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136 <option value="qilo">First nucleotide of the query aligned with the target</option>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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137 <option value="ql">Query sequence length</option>
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138 <option value="qlo">First nucleotide of the query aligned with the target</option>
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139 <option value="qrow">Print the sequence of the query segment as seen in the pairwise alignment</option>
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140 <option value="qs">Query segment length</option>
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141 <option value="qstrand">Query strand orientation (+ or - for nucleotide sequences)</option>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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142 <option value="query" selected="True">Query label</option>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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143 <option value="raw">Raw alignment score (negative, null or positive integer value)</option>
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144 <option value="target" selected="True">Target label</option>
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145 <option value="tcov">Fraction of the target sequence that is aligned with the query sequence</option>
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146 <option value="tframe">Target frame (-3 to +3) - not computed by vsearch</option>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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147 <option value="thi">Last nucleotide of the target aligned with the query</option>
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148 <option value="tihi">Last nucleotide of the target aligned with the query (ignoring terminal gaps)</option>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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149 <option value="tilo">First nucleotide of the target aligned with the query (ignoring initial gaps)</option>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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150 <option value="tl">Target sequence length (positive integer value)</option>
24e4f42410e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit e5cf9d23d3659072c80ad4bc5d6882da9605ab7e
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151 <option value="tlo">First nucleotide of the target aligned with the query</option>
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152 <option value="trow">Print the sequence of the target segment as seen in the pairwise alignment</option>
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153 <option value="ts">Target segment length</option>
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154 <option value="tstrand">Target strand orientation (+ or - for nucleotide sequences)</option>
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155 </param>
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156 </when>
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157 <when value="no" />
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158 </conditional>
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159 </xml>
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160
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161 <xml name="general_output">
8
49daa1e5faf4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 89e3a62dd6cbc8bcec84d08c1710bfb4e7f5938f
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162 <param name="outputs" type="select" multiple="True" optional="false" label="Select output files" help="">
0
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163 <option value="--alnout">Human-readable alignment output</option>
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164 <option value="--blast6out" selected="True">Blast-like tab-separated output</option>
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165 <option value="--fastapairs">Write query/target pairs of sequences</option>
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166 <yield/>
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167 </param>
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168 </xml>
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169
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170 <token name="@EXTERNAL_DOCUMENTATION@">
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171 <![CDATA[
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172
9
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iuc
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173 For details about this tool, please refer to the `GitHub repository <https://github.com/torognes/vsearch>`_ or the `vsearch manual <https://github.com/torognes/vsearch/releases/download/v2.8.3/vsearch_manual.pdf>`_.
0
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174
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175 ]]>
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176 </token>
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177 <token name="@USERFIELDS_HELP@">
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178 **Available fields in user defined tabular output**
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179
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180 ========= ================
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181 Key Description
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182 ========= ================
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183 aln Print a string of M (match), D (delete, i.e. a gap in the query) and I (insert, i.e. a gap in the target) representing the pairwise alignment. Empty field if there is no alignment.
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184 alnlen Print the length of the query-target alignment (number of columns). The field is set to 0 if there is no alignment.
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185 bits Bit score (not computed for nucleotide alignments). Always set to 0.
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186 caln Compact representation of the pairwise alignment using the CIGAR format (Compact Idiosyncratic Gapped Alignment Report): M (match), D (deletion) and I (insertion). Empty field if there is no alignment.
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187 evalue E-value (not computed for nucleotide alignments). Always set to -1.
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188 exts Number of columns containing a gap extension (zero or positive integer value).
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189 gaps Number of columns containing a gap (zero or positive integer value).
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190 id Percentage of identity (real value ranging from 0.0 to 100.0). The percentage identity is defined as 100 * (matching columns) / (alignment length - terminal gaps).
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191 id0 CD-HIT definition of the percentage of identity (real value ranging from 0.0 to 100.0) using the length of the shortest sequence in the pairwise alignment as denominator: 100 * (matching columns) / (shortest sequence length).
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192 id1 The percentage of identity (real value ranging from 0.0 to 100.0) is defined as the edit distance: 100 * (matching columns) / (alignment length).
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193 id2 The percentage of identity (real value ranging from 0.0 to 100.0) is defined as the edit distance, excluding terminal gaps. The field id2 is an alias for the field id.
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194 id3 Marine Biological Lab definition of the percentage of identity (real value ranging from 0.0 to 100.0), counting each extended gap (internal or terminal) as a single difference and using the length of the longest sequence in the pairwise alignment as denominator: 100 * (1.0 - [(mismatches + gaps) / (longest sequence length)]).
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195 id4 BLAST definition of the percentage of identity (real value ranging from 0.0 to 100.0), equivalent to −−iddef 2 in a context of global pairwise alignment.
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196 ids Number of matches in the alignment (zero or positive integer value).
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197 mism Number of mismatches in the alignment (zero or positive integer value).
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198 opens Number of columns containing a gap opening (zero or positive integer value).
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199 pairs Number of columns containing only nucleotides. That value corresponds to the length of the alignment minus the gap-containing columns (zero or positive integer value).
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200 pctgaps Number of columns containing gaps expressed as a percentage of the alignment length (real value ranging from 0.0 to 100.0).
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201 pctpv Percentage of positive columns. When working with nucleotide sequences, this is equivalent to the percentage of matches (real value ranging from 0.0 to 100.0).
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202 pv Number of positive columns. When working with nucleotide sequences, this is equivalent to the number of matches (zero or positive integer value).
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203 qcov Fraction of the query sequence that is aligned with the target sequence (real value ranging from 0.0 to 100.0). The query coverage is computed as 100.0 * (matches + mismatches) / query sequence length. Internal or terminal gaps are not taken into account. The field is set to 0.0 if there is no alignment.
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204 qframe Query frame (-3 to +3). That field only concerns coding sequences and is not computed by vsearch. Always set to +0.
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205 qhi Last nucleotide of the query aligned with the target. Always equal to the length of the pairwise alignment. The field is set to 0 if there is no alignment.
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206 qihi Last nucleotide of the query aligned with the target (ignoring terminal gaps). Nucleotide numbering starts from 1. The field is set to 0 if there is no alignment.
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207 qilo First nucleotide of the query aligned with the target (ignoring initial gaps). Nucleotide numbering starts from 1. The field is set to 0 if there is no alignment.
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208 ql Query sequence length (positive integer value). The field is set to 0 if there is no alignment.
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209 qlo First nucleotide of the query aligned with the target. Always equal to 1 if there is an alignment, 0 otherwise.
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210 qrow Print the sequence of the query segment as seen in the pairwise alignment (i.e. with gap insertions if need be). Empty field if there is no alignment.
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211 qs Query segment length. Always equal to query sequence length.
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212 qstrand Query strand orientation (+ or - for nucleotide sequences). Empty field if there is no alignment.
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213 query Query label.
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214 raw Raw alignment score (negative, null or positive integer value). The score is the sum of match rewards minus mismatch penalties, gap openings and gap extensions. The field is set to 0 if there is no alignment.
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215 target Target label. The field is set to "*" if there is no alignment.
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216 tcov Fraction of the target sequence that is aligned with the query sequence (real value rang-ing from 0.0 to 100.0). The target coverage is computed as 100.0 * (matches + mis-matches) / target sequence length. Internal or terminal gaps are not taken into account. The field is set to 0.0 if there is no alignment.
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217 tframe Target frame (-3 to +3). That field only concerns coding sequences and is not computed by vsearch. Always set to +0.
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218 thi Last nucleotide of the target aligned with the query. Always equal to the length of the pairwise alignment. The field is set to 0 if there is no alignment.
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219 tihi Last nucleotide of the target aligned with the query (ignoring terminal gaps). Nucleotide numbering starts from 1. The field is set to 0 if there is no alignment.
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220 tilo First nucleotide of the target aligned with the query (ignoring initial gaps). Nucleotide numbering starts from 1. The field is set to 0 if there is no alignment.
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221 tl Target sequence length (positive integer value). The field is set to 0 if there is no alignment.
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222 tlo First nucleotide of the target aligned with the query. Always equal to 1 if there is an alignment, 0 otherwise.
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223 trow Print the sequence of the target segment as seen in the pairwise alignment (i.e. with gap insertions if need be). Empty field if there is no alignment.
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224 ts Target segment length. Always equal to target sequence length. The field is set to 0 if there is no alignment.
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225 tstrand Target strand orientation (+ or - for nucleotide sequences). Always set to "+", so reverse strand matches have tstrand "+" and qstrand "-". Empty field if there is no alignment.
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226 ========= ================
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227
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228 </token>
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229 <xml name="citations">
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230 <citations>
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231 <citation type="doi">10.5281/zenodo.15524</citation>
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232 <yield />
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233 </citations>
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234 </xml>
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235 </macros>