Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_macros.xml @ 16:b5f1f599d1fb draft
Uploaded v0.1.04, fix regression with BLAST database from history
author | peterjc |
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date | Wed, 22 Jul 2015 05:01:11 -0400 |
parents | c16c30e9ad5b |
children | 697f40151eaf |
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11
4c4a0da938ff
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1 <macros> |
15
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2 <xml name="preamble"> |
c16c30e9ad5b
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3 <requirements> |
c16c30e9ad5b
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4 <requirement type="binary">@BINARY@</requirement> |
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5 <requirement type="package" version="2.2.30">blast+</requirement> |
c16c30e9ad5b
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6 </requirements> |
c16c30e9ad5b
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7 <stdio> |
c16c30e9ad5b
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8 <!-- Anything other than zero is an error --> |
c16c30e9ad5b
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9 <exit_code range="1:" /> |
c16c30e9ad5b
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10 <!-- Might see negative return codes for Unix signals via Python subprocess --> |
c16c30e9ad5b
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11 <exit_code range=":-1" /> |
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12 <!-- In case the return code has not been set properly check stderr too --> |
c16c30e9ad5b
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13 <regex match="Error:" /> |
c16c30e9ad5b
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peterjc
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14 <regex match="Exception:" /> |
c16c30e9ad5b
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15 </stdio> |
c16c30e9ad5b
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16 <version_command>@BINARY@ -version</version_command> |
c16c30e9ad5b
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17 </xml> |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
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18 <xml name="output_change_format"> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
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19 <change_format> |
13
623f727cdff1
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20 <when input="output.out_format" value="0" format="txt"/> |
623f727cdff1
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peterjc
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21 <when input="output.out_format" value="0 -html" format="html"/> |
623f727cdff1
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peterjc
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22 <when input="output.out_format" value="2" format="txt"/> |
623f727cdff1
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peterjc
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23 <when input="output.out_format" value="2 -html" format="html"/> |
623f727cdff1
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peterjc
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24 <when input="output.out_format" value="4" format="txt"/> |
623f727cdff1
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peterjc
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25 <when input="output.out_format" value="4 -html" format="html"/> |
623f727cdff1
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peterjc
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26 <when input="output.out_format" value="5" format="blastxml"/> |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
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27 </change_format> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
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28 </xml> |
4c4a0da938ff
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peterjc
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29 <xml name="input_out_format"> |
13
623f727cdff1
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30 <conditional name="output"> |
623f727cdff1
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31 <param name="out_format" type="select" label="Output format"> |
623f727cdff1
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peterjc
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32 <option value="6">Tabular (standard 12 columns)</option> |
623f727cdff1
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peterjc
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33 <option value="ext" selected="True">Tabular (extended 25 columns)</option> |
623f727cdff1
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peterjc
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34 <option value="cols">Tabular (select which columns)</option> |
623f727cdff1
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peterjc
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35 <option value="5">BLAST XML</option> |
623f727cdff1
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peterjc
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36 <option value="0">Pairwise text</option> |
623f727cdff1
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peterjc
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37 <option value="0 -html">Pairwise HTML</option> |
623f727cdff1
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peterjc
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38 <option value="2">Query-anchored text</option> |
623f727cdff1
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39 <option value="2 -html">Query-anchored HTML</option> |
623f727cdff1
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40 <option value="4">Flat query-anchored text</option> |
623f727cdff1
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41 <option value="4 -html">Flat query-anchored HTML</option> |
623f727cdff1
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peterjc
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42 <!-- |
623f727cdff1
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43 <option value="-outfmt 11">BLAST archive format (ASN.1)</option> |
623f727cdff1
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44 --> |
623f727cdff1
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peterjc
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45 </param> |
623f727cdff1
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peterjc
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46 <when value="6"/> |
623f727cdff1
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peterjc
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47 <when value="ext"/> |
623f727cdff1
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peterjc
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48 <when value="cols"> |
623f727cdff1
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peterjc
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49 <param name="std_cols" type="select" multiple="true" display="checkboxes" label="Standard columns"> |
623f727cdff1
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peterjc
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50 <option selected="true" value="qseqid">qseqid = Query Seq-id (ID of your sequence)</option> |
623f727cdff1
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peterjc
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51 <option selected="true" value="sseqid">sseqid = Subject Seq-id (ID of the database hit)</option> |
623f727cdff1
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peterjc
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52 <option selected="true" value="pident">pident = Percentage of identical matches</option> |
623f727cdff1
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53 <option selected="true" value="length">length = Alignment length</option> |
623f727cdff1
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54 <option selected="true" value="mismatch">mismatch = Number of mismatches</option> |
623f727cdff1
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55 <option selected="true" value="gapopen">gapopen = Number of gap openings</option> |
623f727cdff1
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56 <option selected="true" value="qstart">qstart = Start of alignment in query</option> |
623f727cdff1
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57 <option selected="true" value="qend">qend = End of alignment in query</option> |
623f727cdff1
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peterjc
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58 <option selected="true" value="sstart">sstart = Start of alignment in subject (database hit)</option> |
623f727cdff1
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peterjc
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59 <option selected="true" value="send">send = End of alignment in subject (database hit)</option> |
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60 <option selected="true" value="evalue">evalue = Expectation value (E-value)</option> |
623f727cdff1
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peterjc
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61 <option selected="true" value="bitscore">bitscore = Bit score</option> |
623f727cdff1
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62 </param> |
623f727cdff1
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peterjc
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63 <param name="ext_cols" type="select" multiple="true" display="checkboxes" label="Extended columns"> |
623f727cdff1
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peterjc
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64 <option value="sallseqid">sallseqid = All subject Seq-id(s), separated by a ';'</option> |
623f727cdff1
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peterjc
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65 <option value="score">score = Raw score</option> |
623f727cdff1
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66 <option value="nident">nident = Number of identical matches</option> |
623f727cdff1
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67 <option value="positive">positive = Number of positive-scoring matches</option> |
623f727cdff1
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68 <option value="gaps">gaps = Total number of gaps</option> |
623f727cdff1
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69 <option value="ppos">ppos = Percentage of positive-scoring matches</option> |
623f727cdff1
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70 <option value="qframe">qframe = Query frame</option> |
623f727cdff1
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71 <option value="sframe">sframe = Subject frame</option> |
623f727cdff1
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72 <option value="qseq">qseq = Aligned part of query sequence</option> |
623f727cdff1
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73 <option value="sseq">sseq = Aligned part of subject sequence</option> |
623f727cdff1
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74 <option value="qlen">qlen = Query sequence length</option> |
623f727cdff1
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75 <option value="slen">slen = Subject sequence length</option> |
623f727cdff1
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76 <option value="salltitles">salltitles = All subject title(s), separated by a '<>'</option> |
623f727cdff1
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77 </param> |
15
c16c30e9ad5b
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78 <param name="ids_cols" type="select" multiple="true" display="checkboxes" label="Other identifier columns"> |
13
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79 <option value="qgi">qgi = Query GI</option> |
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80 <option value="qacc">qacc = Query accesion</option> |
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81 <option value="qaccver">qaccver = Query accesion.version</option> |
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82 <option value="sallseqid">sallseqid = All subject Seq-id(s), separated by a ';'</option> |
623f727cdff1
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83 <option value="sgi">sgi = Subject GI</option> |
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84 <option value="sallgi">sallgi = All subject GIs</option> |
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85 <option value="sacc">sacc = Subject accession</option> |
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86 <option value="saccver">saccver = Subject accession.version</option> |
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87 <option value="sallacc">sallacc = All subject accessions</option> |
623f727cdff1
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88 <option value="stitle">stitle = Subject Title</option> |
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89 </param> |
623f727cdff1
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90 <param name="misc_cols" type="select" multiple="true" display="checkboxes" label="Miscellaneous columns"> |
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91 <option value="sstrand">sstrand = Subject Strand</option> |
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92 <!-- Is it really worth including 'frames' given have 'qframe' and 'sframe'? --> |
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93 <option value="frames">frames = Query and subject frames separated by a '/'</option> |
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94 <option value="btop">btop = Blast traceback operations (BTOP)</option> |
623f727cdff1
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95 <option value="qcovs">qcovs = Query Coverage Per Subject</option> |
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96 <option value="qcovhsp">qcovhsp = Query Coverage Per HSP</option> |
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97 </param> |
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98 <param name="tax_cols" type="select" multiple="true" display="checkboxes" label="Taxonomy columns"> |
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99 <option value="staxids">staxids = unique Subject Taxonomy ID(s), separated by a ';' (in numerical order)</option> |
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100 <!-- TODO, how to handle the taxonomy data file dependency? If missing these give N/A --> |
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101 <option value="sscinames">sscinames = unique Subject Scientific Name(s), separated by a ';'</option> |
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102 <option value="scomnames">scomnames = unique Subject Common Name(s), separated by a ';'</option> |
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103 <option value="sblastnames">sblastnames = unique Subject Blast Name(s), separated by a ';' (in alphabetical order)</option> |
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104 <option value="sskingdoms">sskingdoms = unique Subject Super Kingdom(s), separated by a ';' (in alphabetical order)</option> |
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105 </param> |
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106 </when> |
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107 <when value="5"/> |
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108 <when value="0"/> |
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109 <when value="0 -html"/> |
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110 <when value="2"/> |
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111 <when value="2 -html"/> |
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112 <when value="4"/> |
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113 <when value="4 -html"/> |
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114 </conditional> |
11
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115 </xml> |
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116 <xml name="input_scoring_matrix"> |
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117 <param name="matrix" type="select" label="Scoring matrix"> |
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118 <option value="BLOSUM90">BLOSUM90</option> |
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119 <option value="BLOSUM80">BLOSUM80</option> |
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120 <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option> |
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121 <option value="BLOSUM50">BLOSUM50</option> |
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122 <option value="BLOSUM45">BLOSUM45</option> |
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123 <option value="PAM250">PAM250</option> |
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124 <option value="PAM70">PAM70</option> |
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125 <option value="PAM30">PAM30</option> |
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126 </param> |
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127 </xml> |
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128 <xml name="input_query_gencode"> |
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129 <param name="query_gencode" type="select" label="Query genetic code"> |
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130 <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> |
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131 <option value="1" select="True">1. Standard</option> |
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132 <option value="2">2. Vertebrate Mitochondrial</option> |
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133 <option value="3">3. Yeast Mitochondrial</option> |
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134 <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> |
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135 <option value="5">5. Invertebrate Mitochondrial</option> |
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136 <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option> |
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137 <option value="9">9. Echinoderm Mitochondrial</option> |
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138 <option value="10">10. Euplotid Nuclear</option> |
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139 <option value="11">11. Bacteria and Archaea</option> |
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140 <option value="12">12. Alternative Yeast Nuclear</option> |
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141 <option value="13">13. Ascidian Mitochondrial</option> |
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142 <option value="14">14. Flatworm Mitochondrial</option> |
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143 <option value="15">15. Blepharisma Macronuclear</option> |
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144 <option value="16">16. Chlorophycean Mitochondrial Code</option> |
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145 <option value="21">21. Trematode Mitochondrial Code</option> |
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146 <option value="22">22. Scenedesmus obliquus mitochondrial Code</option> |
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147 <option value="23">23. Thraustochytrium Mitochondrial Code</option> |
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148 <option value="24">24. Pterobranchia mitochondrial code</option> |
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149 </param> |
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150 </xml> |
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151 <xml name="input_db_gencode"> |
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152 <param name="db_gencode" type="select" label="Database/subject genetic code"> |
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153 <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> |
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154 <option value="1" select="True">1. Standard</option> |
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155 <option value="2">2. Vertebrate Mitochondrial</option> |
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156 <option value="3">3. Yeast Mitochondrial</option> |
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157 <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> |
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158 <option value="5">5. Invertebrate Mitochondrial</option> |
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159 <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option> |
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160 <option value="9">9. Echinoderm Mitochondrial</option> |
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161 <option value="10">10. Euplotid Nuclear</option> |
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162 <option value="11">11. Bacteria and Archaea</option> |
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163 <option value="12">12. Alternative Yeast Nuclear</option> |
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164 <option value="13">13. Ascidian Mitochondrial</option> |
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165 <option value="14">14. Flatworm Mitochondrial</option> |
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166 <option value="15">15. Blepharisma Macronuclear</option> |
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167 <option value="16">16. Chlorophycean Mitochondrial Code</option> |
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168 <option value="21">21. Trematode Mitochondrial Code</option> |
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169 <option value="22">22. Scenedesmus obliquus mitochondrial Code</option> |
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170 <option value="23">23. Thraustochytrium Mitochondrial Code</option> |
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171 <option value="24">24. Pterobranchia mitochondrial code</option> |
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172 </param> |
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173 </xml> |
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174 <xml name="input_conditional_nucleotide_db"> |
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175 <conditional name="db_opts"> |
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176 <param name="db_opts_selector" type="select" label="Subject database/sequences"> |
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177 <option value="db" selected="True">Locally installed BLAST database</option> |
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178 <option value="histdb">BLAST database from your history</option> |
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179 <option value="file">FASTA file from your history (see warning note below)</option> |
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180 </param> |
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181 <when value="db"> |
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182 <param name="database" type="select" label="Nucleotide BLAST database"> |
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183 <options from_data_table="blastdb" /> |
11
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184 </param> |
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185 <param name="histdb" type="hidden" value="" /> |
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186 <param name="subject" type="hidden" value="" /> |
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187 </when> |
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188 <when value="histdb"> |
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189 <param name="database" type="hidden" value="" /> |
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190 <param name="histdb" type="data" format="blastdbn" label="Nucleotide BLAST database" /> |
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191 <param name="subject" type="hidden" value="" /> |
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192 </when> |
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193 <when value="file"> |
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194 <param name="database" type="hidden" value="" /> |
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195 <param name="histdb" type="hidden" value="" /> |
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196 <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> |
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197 </when> |
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198 </conditional> |
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199 </xml> |
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200 <xml name="input_conditional_protein_db"> |
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201 <conditional name="db_opts"> |
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202 <param name="db_opts_selector" type="select" label="Subject database/sequences"> |
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203 <option value="db" selected="True">Locally installed BLAST database</option> |
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204 <option value="histdb">BLAST database from your history</option> |
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205 <option value="file">FASTA file from your history (see warning note below)</option> |
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206 </param> |
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207 <when value="db"> |
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208 <param name="database" type="select" label="Protein BLAST database"> |
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209 <options from_data_table="blastdb_p" /> |
11
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210 </param> |
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211 <param name="histdb" type="hidden" value="" /> |
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212 <param name="subject" type="hidden" value="" /> |
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213 </when> |
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214 <when value="histdb"> |
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215 <param name="database" type="hidden" value="" /> |
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216 <param name="histdb" type="data" format="blastdbp" label="Protein BLAST database" /> |
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217 <param name="subject" type="hidden" value="" /> |
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218 </when> |
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219 <when value="file"> |
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220 <param name="database" type="hidden" value="" /> |
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221 <param name="histdb" type="hidden" value="" /> |
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222 <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> |
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223 </when> |
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224 </conditional> |
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225 </xml> |
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226 <xml name="input_conditional_pssm"> |
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227 <conditional name="db_opts"> |
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228 <param name="db_opts_selector" type="select" label="Protein domain database (PSSM)"> |
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2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
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229 <option value="db" selected="True">Locally installed BLAST protein domain database</option> |
11
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230 <option value="histdb">BLAST protein domain database from your history</option> |
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231 </param> |
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232 <when value="db"> |
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233 <param name="database" type="select" label="Protein domain database"> |
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c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
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234 <options from_data_table="blastdb_d" /> |
11
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235 </param> |
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236 <param name="histdb" type="hidden" value="" /> |
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Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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237 <param name="subject" type="hidden" value="" /> |
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238 </when> |
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239 <when value="histdb"> |
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Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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240 <param name="database" type="hidden" value="" /> |
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Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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241 <param name="histdb" type="data" format="blastdbd" label="Protein domain database" /> |
4c4a0da938ff
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242 <param name="subject" type="hidden" value="" /> |
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Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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243 </when> |
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244 </conditional> |
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245 </xml> |
4c4a0da938ff
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246 <xml name="input_conditional_choose_db_type"> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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247 <conditional name="db_opts"> |
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248 <param name="db_type" type="select" label="Type of BLAST database"> |
4c4a0da938ff
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249 <option value="nucl" selected="True">Nucleotide</option> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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250 <option value="prot">Protein</option> |
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251 </param> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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252 <when value="nucl"> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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253 <param name="database" type="select" label="Nucleotide BLAST database"> |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
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254 <options from_data_table="blastdb" /> |
11
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Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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parents:
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255 </param> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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256 </when> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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257 <when value="prot"> |
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Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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258 <param name="database" type="select" label="Protein BLAST database"> |
15
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Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
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259 <options from_data_table="blastdb_p" /> |
11
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260 </param> |
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261 </when> |
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262 </conditional> |
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263 </xml> |
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Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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264 <xml name="input_parse_deflines"> |
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Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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265 <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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266 </xml> |
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Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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267 <xml name="input_filter_query_default_false"> |
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268 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" /> |
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269 </xml> |
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270 <xml name="input_filter_query_default_true"> |
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271 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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272 </xml> |
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Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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273 <xml name="input_max_hits"> |
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274 <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> |
4c4a0da938ff
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275 <validator type="in_range" min="0" /> |
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Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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276 </param> |
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277 </xml> |
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278 <xml name="input_evalue"> |
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279 <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> |
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280 </xml> |
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281 <xml name="input_word_size"> |
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282 <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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283 <validator type="in_range" min="0" /> |
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Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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284 </param> |
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285 </xml> |
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Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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286 <xml name="input_strand"> |
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287 <param name="strand" type="select" label="Query strand(s) to search against database/subject"> |
4c4a0da938ff
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288 <option value="-strand both">Both</option> |
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289 <option value="-strand plus">Plus (forward)</option> |
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290 <option value="-strand minus">Minus (reverse complement)</option> |
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291 </param> |
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292 </xml> |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
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293 <xml name="input_qcov_hsp_perc"> |
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Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
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294 <param name="qcov_hsp_perc" type="float" value="0" min="0" max="100" label="Minimum query coverage per hsp (percentage, 0 to 100)" help="See also the output column qhspcov"/> |
11
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parents:
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295 </xml> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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parents:
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296 <xml name="advanced_options"> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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parents:
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297 <conditional name="adv_opts"> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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298 <param name="adv_opts_selector" type="select" label="Advanced Options"> |
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Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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299 <option value="basic" selected="True">Hide Advanced Options</option> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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300 <option value="advanced">Show Advanced Options</option> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
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301 </param> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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302 <when value="basic" /> |
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Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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303 <when value="advanced"> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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304 <yield /> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
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305 </when> |
14
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
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306 </conditional> |
11
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peterjc
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307 </xml> |
14
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
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308 <xml name="advanced_optional_id_files"> |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
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309 <conditional name="adv_optional_id_files_opts"> |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
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310 <param name="adv_optional_id_files_opts_selector" type="select" |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
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311 label="Restrict search of database to a given set of ID's" |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
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312 help="This feature provides a means to exclude ID's from a BLAST database search. The expectation values in the BLAST results are based upon the sequences actually searched, and not on the underlying database. Note this cannot be used when comparing against a FASTA file."> |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
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313 <option value="none" selected="True">No restriction, search the entire database</option> |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
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314 <option value="gilist">GI identifiers</option> |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
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315 <option value="negative_gilist">Negative GI identifiers</option> |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
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316 <option value="seqidlist">Sequence identifiers (SeqId's)</option> |
14
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
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317 </param> |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
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318 <when value="none" /> |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
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319 <when value="gilist"> |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
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320 <param name="gilist" type="data" format="txt" label="Restrict search of database to GI's listed in this file" |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
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321 help="This option is only available for database searches."/> |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
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322 </when> |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
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323 <when value="negative_gilist"> |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
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324 <param name="negative_gilist" type="data" format="txt" label="Restrict search of database to everything except the GI's listed in this file" |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
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325 help="This option is only available for database searches."/> |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
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326 </when> |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
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327 <when value="seqidlist"> |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
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328 <param name="seqidlist" type="data" format="txt" label=" Restrict search of database to list of SeqId's" |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
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329 help="This option is only available for database searches."/> |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
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330 </when> |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
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331 </conditional> |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
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332 </xml> |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
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333 <token name="@ADV_QCOV_HSP_PERC@"> |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
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334 #if float(str($adv_opts.qcov_hsp_perc)) > 0: |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
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335 -qcov_hsp_perc $adv_opts.qcov_hsp_perc |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
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336 #end if |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
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337 </token> |
14
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
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338 <token name="@ADV_ID_LIST_FILTER@"> |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
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339 #if $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'negative_gilist': |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
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340 -negative_gilist $adv_opts.adv_optional_id_files_opts.negative_gilist |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
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341 #elif $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'gilist': |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
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342 -gilist $adv_opts.adv_optional_id_files_opts.gilist |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
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343 #elif $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'seqidlist': |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
13
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344 -seqidlist $adv_opts.adv_optional_id_files_opts.seqidlist |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
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345 #end if |
2fe07f50a41e
Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.
peterjc
parents:
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346 </token> |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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347 <token name="@THREADS@">-num_threads "\${GALAXY_SLOTS:-8}"</token> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
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348 <token name="@BLAST_DB_SUBJECT@"> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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349 #if $db_opts.db_opts_selector == "db": |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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350 -db "${db_opts.database.fields.path}" |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
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351 #elif $db_opts.db_opts_selector == "histdb": |
16
b5f1f599d1fb
Uploaded v0.1.04, fix regression with BLAST database from history
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352 -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}" |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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353 #else: |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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354 -subject "$db_opts.subject" |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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355 #end if |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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|
356 </token> |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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357 <token name="@BLAST_OUTPUT@">-out "$output1" |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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|
358 ##Set the extended list here so when we add things, saved workflows are not affected |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
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359 #if str($output.out_format)=="ext": |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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|
360 -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen salltitles" |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
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361 #elif str($output.out_format)=="cols" |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
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362 ##Pick your own columns. Galaxy gives us it comma separated, BLAST+ wants space separated: |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
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363 ##TODO - Can we catch the user picking no columns and raise an error here? |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
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|
364 #set cols = (str($output.std_cols)+","+str($output.ext_cols)+","+str($output.ids_cols)+","+str($output.misc_cols)+","+str($output.tax_cols)).replace("None", "").replace(",,", ",").replace(",", " ").strip() |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
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|
365 -outfmt "6 $cols" |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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|
366 #else: |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
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|
367 -outfmt $output.out_format |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
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368 #end if |
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
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|
369 </token> |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
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14
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370 <token name="@ADV_FILTER_QUERY@">$adv_opts.filter_query</token> |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
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371 <token name="@ADV_MAX_HITS@"> |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
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|
372 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
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|
373 ## Note -max_target_seqs used to simply override -num_descriptions and -num_alignments |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
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|
374 ## but this was changed in BLAST+ 2.2.27 onwards to force their use (raised with NCBI) |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
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375 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): |
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376 #if str($output.out_format) in ["6", "ext", "cols", "5"]: |
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377 ## Most output formats use this, including tabular and XML: |
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378 -max_target_seqs $adv_opts.max_hits |
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379 #else |
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380 ## Text and HTML output formats 0-4 currently need this instead: |
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381 -num_descriptions $adv_opts.max_hits -num_alignments $adv_opts.max_hits |
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382 #end if |
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383 #end if |
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384 </token> |
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385 <token name="@ADV_WORD_SIZE@"> |
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386 #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): |
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387 -word_size $adv_opts.word_size |
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388 #end if |
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389 $adv_opts.parse_deflines |
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390 </token> |
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391 <!-- @ON_DB_SUBJECT@ is for use with @BLAST_DB_SUBJECT@ --> |
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392 <token name="@ON_DB_SUBJECT@">#if str($db_opts.db_opts_selector)=='db' |
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393 ${db_opts.database} |
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394 #elif str($db_opts.db_opts_selector)=='histdb' |
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395 ${db_opts.histdb.name} |
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396 #else |
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397 ${db_opts.subject.name} |
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398 #end if</token> |
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399 <token name="@REFERENCES@"> |
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400 Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo (2015). |
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401 NCBI BLAST+ integrated into Galaxy. *BioRxiv* preprint. |
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402 http://dx.doi.org/10.1101/014043 |
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403 |
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404 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). |
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405 Galaxy tools and workflows for sequence analysis with applications |
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406 in molecular plant pathology. *PeerJ* 1:e167 |
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407 http://dx.doi.org/10.7717/peerj.167 |
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408 |
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409 Christiam Camacho et al. (2009). |
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410 BLAST+: architecture and applications. |
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411 *BMC Bioinformatics*. 15;10:421. |
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412 http://dx.doi.org/10.1186/1471-2105-10-421 |
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413 |
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414 This wrapper is available to install into other Galaxy Instances via the Galaxy |
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415 Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus |
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416 </token> |
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417 <xml name="blast_citations"> |
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418 <citations> |
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419 <citation type="doi">10.1186/1471-2105-10-421</citation> |
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420 <citation type="doi">10.7717/peerj.167</citation> |
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421 <!-- TODO - remove PeerJ paper once "NCBI BLAST+ integrated into Galaxy" formally published? --> |
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422 <citation type="doi">10.1101/014043</citation> |
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423 <!-- TODO - Update DOI once "NCBI BLAST+ integrated into Galaxy" formally published --> |
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424 </citations> |
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425 </xml> |
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426 <token name="@OUTPUT_FORMAT@">**Output format** |
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427 |
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428 Because Galaxy focuses on processing tabular data, the default output of this |
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429 tool is tabular. The standard BLAST+ tabular output contains 12 columns: |
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430 |
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431 ====== ========= ============================================ |
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432 Column NCBI name Description |
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433 ------ --------- -------------------------------------------- |
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434 1 qseqid Query Seq-id (ID of your sequence) |
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435 2 sseqid Subject Seq-id (ID of the database hit) |
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436 3 pident Percentage of identical matches |
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437 4 length Alignment length |
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438 5 mismatch Number of mismatches |
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439 6 gapopen Number of gap openings |
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440 7 qstart Start of alignment in query |
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441 8 qend End of alignment in query |
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442 9 sstart Start of alignment in subject (database hit) |
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443 10 send End of alignment in subject (database hit) |
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444 11 evalue Expectation value (E-value) |
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445 12 bitscore Bit score |
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446 ====== ========= ============================================ |
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447 |
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448 The BLAST+ tools can optionally output additional columns of information, |
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449 but this takes longer to calculate. Many commonly used extra columns are |
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450 included by selecting the extended tabular output. The extra columns are |
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451 included *after* the standard 12 columns. This is so that you can write |
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452 workflow filtering steps that accept either the 12 or 25 column tabular |
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453 BLAST output. Galaxy now uses this extended 25 column output by default. |
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454 |
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455 ====== ============= =========================================== |
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456 Column NCBI name Description |
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457 ------ ------------- ------------------------------------------- |
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458 13 sallseqid All subject Seq-id(s), separated by a ';' |
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459 14 score Raw score |
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460 15 nident Number of identical matches |
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461 16 positive Number of positive-scoring matches |
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462 17 gaps Total number of gaps |
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463 18 ppos Percentage of positive-scoring matches |
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464 19 qframe Query frame |
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465 20 sframe Subject frame |
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466 21 qseq Aligned part of query sequence |
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467 22 sseq Aligned part of subject sequence |
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468 23 qlen Query sequence length |
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469 24 slen Subject sequence length |
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470 25 salltitles All subject title(s), separated by a '<>' |
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471 ====== ============= =========================================== |
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472 |
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473 The third option is to customise the tabular output by selecting which |
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474 columns you want, from the standard set of 12, the default set of 25, |
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475 or any of the additional columns BLAST+ offers (including species name). |
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Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
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476 |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
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477 The fourth option is BLAST XML output, which is designed to be parsed by |
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478 another program, and is understood by some Galaxy tools. |
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479 |
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480 You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). |
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481 The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. |
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482 The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. |
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483 The two query anchored outputs show a multiple sequence alignment between the query and all the matches, |
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484 and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). |
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485 </token> |
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486 <token name="@FASTA_WARNING@">.. class:: warningmark |
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peterjc
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487 |
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488 You can also search against a FASTA file of subject (target) |
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489 sequences. This is *not* advised because it is slower (only one |
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490 CPU is used), but more importantly gives e-values for pairwise |
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peterjc
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491 searches (very small e-values which will look overly signficiant). |
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492 In most cases you should instead turn the other FASTA file into a |
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493 database first using *makeblastdb* and search against that. |
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494 </token> |
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495 <token name="@SEARCH_TIME_WARNING@">.. class:: warningmark |
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496 |
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497 **Note**. Database searches may take a substantial amount of time. |
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498 For large input datasets it is advisable to allow overnight processing. |
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499 |
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500 ----- |
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501 </token> |
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502 </macros> |