Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_macros.xml @ 23:31e517610e1f draft
v0.3.0 Updated for NCBI BLAST+ 2.7.1
author | peterjc |
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date | Sat, 30 Jun 2018 17:22:46 -0400 |
parents | 6f386c5dc4fb |
children | e25d3acf6e68 |
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1 <macros> |
23 | 2 <token name="@WRAPPER_VERSION@">0.3.0</token> |
17
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3 <xml name="parallelism"> |
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4 <!-- If job splitting is enabled, break up the query file into parts --> |
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5 <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1" /> |
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6 </xml> |
23 | 7 |
15
c16c30e9ad5b
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8 <xml name="preamble"> |
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9 <requirements> |
23 | 10 <requirement type="package" version="2.7.1">blast</requirement> |
15
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11 </requirements> |
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12 <version_command>@BINARY@ -version</version_command> |
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13 </xml> |
23 | 14 |
11
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15 <xml name="output_change_format"> |
4c4a0da938ff
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16 <change_format> |
13
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17 <when input="output.out_format" value="0" format="txt"/> |
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18 <when input="output.out_format" value="0 -html" format="html"/> |
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19 <when input="output.out_format" value="2" format="txt"/> |
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20 <when input="output.out_format" value="2 -html" format="html"/> |
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21 <when input="output.out_format" value="4" format="txt"/> |
623f727cdff1
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22 <when input="output.out_format" value="4 -html" format="html"/> |
623f727cdff1
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23 <when input="output.out_format" value="5" format="blastxml"/> |
11
4c4a0da938ff
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24 </change_format> |
4c4a0da938ff
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25 </xml> |
23 | 26 |
11
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27 <xml name="input_out_format"> |
13
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28 <conditional name="output"> |
22
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29 <param name="out_format" argument="-outfmt" type="select" label="Output format"> |
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30 <option value="6">Tabular (standard 12 columns)</option> |
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31 <option value="ext" selected="true">Tabular (extended 25 columns)</option> |
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32 <option value="cols">Tabular (select which columns)</option> |
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33 <option value="5">BLAST XML</option> |
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34 <option value="0">Pairwise text</option> |
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35 <option value="0 -html">Pairwise HTML</option> |
623f727cdff1
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36 <option value="2">Query-anchored text</option> |
623f727cdff1
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37 <option value="2 -html">Query-anchored HTML</option> |
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38 <option value="4">Flat query-anchored text</option> |
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39 <option value="4 -html">Flat query-anchored HTML</option> |
623f727cdff1
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40 <!-- |
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41 <option value="-outfmt 11">BLAST archive format (ASN.1)</option> |
623f727cdff1
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42 --> |
623f727cdff1
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43 </param> |
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44 <when value="6"/> |
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45 <when value="ext"/> |
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46 <when value="cols"> |
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47 <param name="std_cols" type="select" multiple="true" display="checkboxes" label="Standard columns"> |
623f727cdff1
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48 <option selected="true" value="qseqid">qseqid = Query Seq-id (ID of your sequence)</option> |
623f727cdff1
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49 <option selected="true" value="sseqid">sseqid = Subject Seq-id (ID of the database hit)</option> |
623f727cdff1
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50 <option selected="true" value="pident">pident = Percentage of identical matches</option> |
623f727cdff1
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51 <option selected="true" value="length">length = Alignment length</option> |
623f727cdff1
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52 <option selected="true" value="mismatch">mismatch = Number of mismatches</option> |
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53 <option selected="true" value="gapopen">gapopen = Number of gap openings</option> |
623f727cdff1
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54 <option selected="true" value="qstart">qstart = Start of alignment in query</option> |
623f727cdff1
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55 <option selected="true" value="qend">qend = End of alignment in query</option> |
623f727cdff1
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56 <option selected="true" value="sstart">sstart = Start of alignment in subject (database hit)</option> |
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57 <option selected="true" value="send">send = End of alignment in subject (database hit)</option> |
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58 <option selected="true" value="evalue">evalue = Expectation value (E-value)</option> |
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59 <option selected="true" value="bitscore">bitscore = Bit score</option> |
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60 </param> |
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61 <param name="ext_cols" type="select" multiple="true" display="checkboxes" label="Extended columns"> |
623f727cdff1
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62 <option value="sallseqid">sallseqid = All subject Seq-id(s), separated by a ';'</option> |
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63 <option value="score">score = Raw score</option> |
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64 <option value="nident">nident = Number of identical matches</option> |
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65 <option value="positive">positive = Number of positive-scoring matches</option> |
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66 <option value="gaps">gaps = Total number of gaps</option> |
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67 <option value="ppos">ppos = Percentage of positive-scoring matches</option> |
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68 <option value="qframe">qframe = Query frame</option> |
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69 <option value="sframe">sframe = Subject frame</option> |
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70 <option value="qseq">qseq = Aligned part of query sequence</option> |
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71 <option value="sseq">sseq = Aligned part of subject sequence</option> |
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72 <option value="qlen">qlen = Query sequence length</option> |
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73 <option value="slen">slen = Subject sequence length</option> |
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74 <option value="salltitles">salltitles = All subject title(s), separated by a '<>'</option> |
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75 </param> |
15
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76 <param name="ids_cols" type="select" multiple="true" display="checkboxes" label="Other identifier columns"> |
13
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77 <option value="qgi">qgi = Query GI</option> |
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78 <option value="qacc">qacc = Query accesion</option> |
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79 <option value="qaccver">qaccver = Query accesion.version</option> |
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80 <option value="sallseqid">sallseqid = All subject Seq-id(s), separated by a ';'</option> |
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81 <option value="sgi">sgi = Subject GI</option> |
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82 <option value="sallgi">sallgi = All subject GIs</option> |
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83 <option value="sacc">sacc = Subject accession</option> |
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84 <option value="saccver">saccver = Subject accession.version</option> |
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85 <option value="sallacc">sallacc = All subject accessions</option> |
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86 <option value="stitle">stitle = Subject Title</option> |
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87 </param> |
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88 <param name="misc_cols" type="select" multiple="true" display="checkboxes" label="Miscellaneous columns"> |
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89 <option value="sstrand">sstrand = Subject Strand</option> |
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90 <!-- Is it really worth including 'frames' given have 'qframe' and 'sframe'? --> |
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91 <option value="frames">frames = Query and subject frames separated by a '/'</option> |
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92 <option value="btop">btop = Blast traceback operations (BTOP)</option> |
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93 <option value="qcovs">qcovs = Query Coverage Per Subject</option> |
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94 <option value="qcovhsp">qcovhsp = Query Coverage Per HSP</option> |
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95 </param> |
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96 <param name="tax_cols" type="select" multiple="true" display="checkboxes" label="Taxonomy columns"> |
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97 <option value="staxids">staxids = unique Subject Taxonomy ID(s), separated by a ';' (in numerical order)</option> |
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98 <!-- TODO, how to handle the taxonomy data file dependency? If missing these give N/A --> |
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99 <option value="sscinames">sscinames = unique Subject Scientific Name(s), separated by a ';'</option> |
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100 <option value="scomnames">scomnames = unique Subject Common Name(s), separated by a ';'</option> |
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101 <option value="sblastnames">sblastnames = unique Subject Blast Name(s), separated by a ';' (in alphabetical order)</option> |
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102 <option value="sskingdoms">sskingdoms = unique Subject Super Kingdom(s), separated by a ';' (in alphabetical order)</option> |
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103 </param> |
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104 </when> |
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105 <when value="5"/> |
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106 <when value="0"/> |
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107 <when value="0 -html"/> |
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108 <when value="2"/> |
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109 <when value="2 -html"/> |
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110 <when value="4"/> |
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111 <when value="4 -html"/> |
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112 </conditional> |
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113 </xml> |
23 | 114 |
115 <xml name="input_matrix_gapcosts"> | |
116 <conditional name="matrix_gapcosts"> | |
117 <param argument="-matrix" type="select" label="Scoring matrix and gap costs"> | |
118 <option value="" selected="true">Use Defaults</option> | |
119 <option value="BLOSUM90">BLOSUM90</option> | |
120 <option value="BLOSUM80">BLOSUM80</option> | |
121 <option value="BLOSUM62">BLOSUM62</option> | |
122 <option value="BLOSUM50">BLOSUM50</option> | |
123 <option value="BLOSUM45">BLOSUM45</option> | |
124 <option value="PAM250">PAM250</option> | |
125 <option value="PAM70">PAM70</option> | |
126 <option value="PAM30">PAM30</option> | |
127 </param> | |
128 <when value=""> | |
129 <!-- do nothing --> | |
130 </when> | |
131 <when value="BLOSUM90"> | |
132 <param name="gap_costs" type="select" label="Gap Costs"> | |
133 <option value="" selected="true">Use defaults</option> | |
134 <option value="-gapopen 9 -gapextend 2">Existence: 9 Extension: 2</option> | |
135 <option value="-gapopen 8 -gapextend 2">Existence: 8 Extension: 2</option> | |
136 <option value="-gapopen 7 -gapextend 2">Existence: 7 Extension: 2</option> | |
137 <option value="-gapopen 6 -gapextend 2">Existence: 6 Extension: 2</option> | |
138 <option value="-gapopen 11 -gapextend 1">Existence: 11 Extension: 1</option> | |
139 <option value="-gapopen 10 -gapextend 1">Existence: 10 Extension: 1</option> | |
140 <option value="-gapopen 9 -gapextend 1">Existence: 9 Extension: 1</option> | |
141 </param> | |
142 | |
143 </when> | |
144 <when value="BLOSUM80"> | |
145 <param name="gap_costs" type="select" label="Gap Costs"> | |
146 <option value="" selected="true">Use defaults</option> | |
147 <option value="-gapopen 8 -gapextend 2">Existence: 8 Extension: 2</option> | |
148 <option value="-gapopen 7 -gapextend 2">Existence: 7 Extension: 2</option> | |
149 <option value="-gapopen 6 -gapextend 2">Existence: 6 Extension: 2</option> | |
150 <option value="-gapopen 11 -gapextend 1">Existence: 11 Extension: 1</option> | |
151 <option value="-gapopen 10 -gapextend 1">Existence: 10 Extension: 1</option> | |
152 <option value="-gapopen 9 -gapextend 1">Existence: 9 Extension: 1</option> | |
153 </param> | |
154 </when> | |
155 <when value="BLOSUM62"> | |
156 <param name="gap_costs" type="select" label="Gap Costs"> | |
157 <option value="" selected="true">Use defaults</option> | |
158 <option value="-gapopen 11 -gapextend 2">Existence: 11 Extension: 2</option> | |
159 <option value="-gapopen 10 -gapextend 2">Existence: 10 Extension: 2</option> | |
160 <option value="-gapopen 9 -gapextend 2">Existence: 9 Extension: 2</option> | |
161 <option value="-gapopen 8 -gapextend 2">Existence: 8 Extension: 2</option> | |
162 <option value="-gapopen 7 -gapextend 2">Existence: 7 Extension: 2</option> | |
163 <option value="-gapopen 6 -gapextend 2">Existence: 6 Extension: 2</option> | |
164 <option value="-gapopen 13 -gapextend 1">Existence: 13 Extension: 1</option> | |
165 <option value="-gapopen 12 -gapextend 1">Existence: 12 Extension: 1</option> | |
166 <option value="-gapopen 11 -gapextend 1">Existence: 11 Extension: 1</option> | |
167 <option value="-gapopen 10 -gapextend 1">Existence: 10 Extension: 1</option> | |
168 <option value="-gapopen 9 -gapextend 1">Existence: 9 Extension: 1</option> | |
169 </param> | |
170 | |
171 </when> | |
172 <when value="BLOSUM50"> | |
173 <param name="gap_costs" type="select" label="Gap Costs"> | |
174 <option value="" selected="true">Use defaults</option> | |
175 <option value="-gapopen 13 -gapextend 3">Existence: 13 Extension: 3</option> | |
176 <option value="-gapopen 12 -gapextend 3">Existence: 12 Extension: 3</option> | |
177 <option value="-gapopen 11 -gapextend 3">Existence: 11 Extension: 3</option> | |
178 <option value="-gapopen 10 -gapextend 3">Existence: 10 Extension: 3</option> | |
179 <option value="-gapopen 9 -gapextend 3">Existence: 9 Extension: 3</option> | |
180 <option value="-gapopen 16 -gapextend 2">Existence: 16 Extension: 2</option> | |
181 <option value="-gapopen 15 -gapextend 2">Existence: 15 Extension: 2</option> | |
182 <option value="-gapopen 14 -gapextend 2">Existence: 14 Extension: 2</option> | |
183 <option value="-gapopen 13 -gapextend 2">Existence: 13 Extension: 2</option> | |
184 <option value="-gapopen 12 -gapextend 2">Existence: 12 Extension: 2</option> | |
185 <option value="-gapopen 19 -gapextend 1">Existence: 19 Extension: 1</option> | |
186 <option value="-gapopen 18 -gapextend 1">Existence: 18 Extension: 1</option> | |
187 <option value="-gapopen 17 -gapextend 1">Existence: 17 Extension: 1</option> | |
188 <option value="-gapopen 16 -gapextend 1">Existence: 16 Extension: 1</option> | |
189 <option value="-gapopen 15 -gapextend 1">Existence: 15 Extension: 1</option> | |
190 </param> | |
191 | |
192 </when> | |
193 <when value="BLOSUM45"> | |
194 <param name="gap_costs" type="select" label="Gap Costs"> | |
195 <option value="" selected="true">Use defaults</option> | |
196 <option value="-gapopen 13 -gapextend 3">Existence: 13 Extension: 3</option> | |
197 <option value="-gapopen 12 -gapextend 3">Existence: 12 Extension: 3</option> | |
198 <option value="-gapopen 11 -gapextend 3">Existence: 11 Extension: 3</option> | |
199 <option value="-gapopen 10 -gapextend 3">Existence: 10 Extension: 3</option> | |
200 <option value="-gapopen 15 -gapextend 2">Existence: 15 Extension: 2</option> | |
201 <option value="-gapopen 14 -gapextend 2">Existence: 14 Extension: 2</option> | |
202 <option value="-gapopen 13 -gapextend 2">Existence: 13 Extension: 2</option> | |
203 <option value="-gapopen 12 -gapextend 2">Existence: 12 Extension: 2</option> | |
204 <option value="-gapopen 19 -gapextend 1">Existence: 19 Extension: 1</option> | |
205 <option value="-gapopen 18 -gapextend 1">Existence: 18 Extension: 1</option> | |
206 <option value="-gapopen 17 -gapextend 1">Existence: 17 Extension: 1</option> | |
207 <option value="-gapopen 16 -gapextend 1">Existence: 16 Extension: 1</option> | |
208 </param> | |
209 </when> | |
210 <when value="PAM250"> | |
211 <param name="gap_costs" type="select" label="Gap Costs"> | |
212 <option value="" selected="true">Use defaults</option> | |
213 <option value="-gapopen 15 -gapextend 3">Existence: 15 Extension: 3</option> | |
214 <option value="-gapopen 14 -gapextend 3">Existence: 14 Extension: 3</option> | |
215 <option value="-gapopen 13 -gapextend 3">Existence: 13 Extension: 3</option> | |
216 <option value="-gapopen 12 -gapextend 3">Existence: 12 Extension: 3</option> | |
217 <option value="-gapopen 17 -gapextend 2">Existence: 17 Extension: 2</option> | |
218 <option value="-gapopen 16 -gapextend 2">Existence: 16 Extension: 2</option> | |
219 <option value="-gapopen 15 -gapextend 2">Existence: 15 Extension: 2</option> | |
220 <option value="-gapopen 14 -gapextend 2">Existence: 14 Extension: 2</option> | |
221 <option value="-gapopen 13 -gapextend 2">Existence: 13 Extension: 2</option> | |
222 <option value="-gapopen 21 -gapextend 1">Existence: 21 Extension: 1</option> | |
223 <option value="-gapopen 20 -gapextend 1">Existence: 20 Extension: 1</option> | |
224 <option value="-gapopen 19 -gapextend 1">Existence: 19 Extension: 1</option> | |
225 <option value="-gapopen 18 -gapextend 1">Existence: 18 Extension: 1</option> | |
226 <option value="-gapopen 17 -gapextend 1">Existence: 17 Extension: 1</option> | |
227 </param> | |
228 | |
229 </when> | |
230 <when value="PAM70"> | |
231 <param name="gap_costs" type="select" label="Gap Costs"> | |
232 <option value="" selected="true">Use defaults</option> | |
233 <option value="-gapopen 12 -gapextend 3">Existence: 12 Extension: 3</option> | |
234 <option value="-gapopen 11 -gapextend 2">Existence: 11 Extension: 2</option> | |
235 <option value="-gapopen 8 -gapextend 2">Existence: 8 Extension: 2</option> | |
236 <option value="-gapopen 7 -gapextend 2">Existence: 7 Extension: 2</option> | |
237 <option value="-gapopen 6 -gapextend 2">Existence: 6 Extension: 2</option> | |
238 <option value="-gapopen 11 -gapextend 1">Existence: 11 Extension: 1</option> | |
239 <option value="-gapopen 10 -gapextend 1">Existence: 10 Extension: 1</option> | |
240 <option value="-gapopen 9 -gapextend 1">Existence: 9 Extension: 1</option> | |
241 </param> | |
242 | |
243 </when> | |
244 <when value="PAM30"> | |
245 <param name="gap_costs" type="select" label="Gap Costs"> | |
246 <option value="" selected="true">Use defaults</option> | |
247 <option value="-gapopen 15 -gapextend 3">Existence: 15 Extension: 3</option> | |
248 <option value="-gapopen 13 -gapextend 3">Existence: 13 Extension: 3</option> | |
249 <option value="-gapopen 14 -gapextend 2">Existence: 14 Extension: 2</option> | |
250 <option value="-gapopen 7 -gapextend 2">Existence: 7 Extension: 2</option> | |
251 <option value="-gapopen 6 -gapextend 2">Existence: 6 Extension: 2</option> | |
252 <option value="-gapopen 5 -gapextend 2">Existence: 5 Extension: 2</option> | |
253 <option value="-gapopen 14 -gapextend 1">Existence: 14 Extension: 1</option> | |
254 <option value="-gapopen 10 -gapextend 1">Existence: 10 Extension: 1</option> | |
255 <option value="-gapopen 9 -gapextend 1">Existence: 9 Extension: 1</option> | |
256 <option value="-gapopen 8 -gapextend 1">Existence: 8 Extension: 1</option> | |
257 </param> | |
258 </when> | |
259 </conditional> | |
260 </xml> | |
261 <!-- these gapopen and gapextend macros are only used in blastn. | |
262 otherwise, the combined matrix/gapcosts macro is used --> | |
263 <xml name="input_gapopen"> | |
264 <param argument="-gapopen" type="integer" optional="true" min="0" | |
265 label="Cost to open a gap" | |
266 help="Leave blank for default. See tool help for defaults."/> | |
267 </xml> | |
268 | |
269 <xml name="input_gapextend"> | |
270 <param argument="-gapextend" type="integer" optional="true" min="1" | |
271 label="Cost to extend a gap" | |
272 help="Leave blank for default. See tool help for defaults."/> | |
273 </xml> | |
274 | |
275 <!-- this matrix macro is used in deltablast, makeprofiledb, psiblast, and tblastx --> | |
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276 <xml name="input_scoring_matrix"> |
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277 <param argument="-matrix" type="select" label="Scoring matrix"> |
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278 <option value="BLOSUM90">BLOSUM90</option> |
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279 <option value="BLOSUM80">BLOSUM80</option> |
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280 <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option> |
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281 <option value="BLOSUM50">BLOSUM50</option> |
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282 <option value="BLOSUM45">BLOSUM45</option> |
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283 <option value="PAM250">PAM250</option> |
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284 <option value="PAM70">PAM70</option> |
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285 <option value="PAM30">PAM30</option> |
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286 </param> |
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287 </xml> |
23 | 288 |
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289 <xml name="input_query_gencode"> |
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290 <param argument="-query_gencode" type="select" label="Query genetic code"> |
23 | 291 <!-- See https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> |
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292 <option value="1" selected="true">1. Standard</option> |
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293 <option value="2">2. Vertebrate Mitochondrial</option> |
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294 <option value="3">3. Yeast Mitochondrial</option> |
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295 <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> |
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296 <option value="5">5. Invertebrate Mitochondrial</option> |
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297 <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option> |
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298 <option value="9">9. Echinoderm Mitochondrial</option> |
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299 <option value="10">10. Euplotid Nuclear</option> |
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300 <option value="11">11. Bacteria and Archaea</option> |
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301 <option value="12">12. Alternative Yeast Nuclear</option> |
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302 <option value="13">13. Ascidian Mitochondrial</option> |
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303 <option value="14">14. Flatworm Mitochondrial</option> |
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304 <option value="15">15. Blepharisma Macronuclear</option> |
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305 <option value="16">16. Chlorophycean Mitochondrial Code</option> |
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306 <option value="21">21. Trematode Mitochondrial Code</option> |
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307 <option value="22">22. Scenedesmus obliquus mitochondrial Code</option> |
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308 <option value="23">23. Thraustochytrium Mitochondrial Code</option> |
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309 <option value="24">24. Pterobranchia mitochondrial code</option> |
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310 </param> |
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311 </xml> |
23 | 312 |
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313 <xml name="input_db_gencode"> |
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314 <param argument="-db_gencode" type="select" label="Database/subject genetic code"> |
23 | 315 <!-- See https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> |
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316 <option value="1" selected="true">1. Standard</option> |
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317 <option value="2">2. Vertebrate Mitochondrial</option> |
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318 <option value="3">3. Yeast Mitochondrial</option> |
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319 <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> |
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320 <option value="5">5. Invertebrate Mitochondrial</option> |
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321 <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option> |
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322 <option value="9">9. Echinoderm Mitochondrial</option> |
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323 <option value="10">10. Euplotid Nuclear</option> |
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324 <option value="11">11. Bacteria and Archaea</option> |
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325 <option value="12">12. Alternative Yeast Nuclear</option> |
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326 <option value="13">13. Ascidian Mitochondrial</option> |
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327 <option value="14">14. Flatworm Mitochondrial</option> |
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328 <option value="15">15. Blepharisma Macronuclear</option> |
4c4a0da938ff
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329 <option value="16">16. Chlorophycean Mitochondrial Code</option> |
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330 <option value="21">21. Trematode Mitochondrial Code</option> |
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331 <option value="22">22. Scenedesmus obliquus mitochondrial Code</option> |
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332 <option value="23">23. Thraustochytrium Mitochondrial Code</option> |
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333 <option value="24">24. Pterobranchia mitochondrial code</option> |
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334 </param> |
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335 </xml> |
23 | 336 |
11
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337 <xml name="input_conditional_nucleotide_db"> |
22
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338 <!-- Usually database argument mapped to -db, but -in in dustmasker --> |
11
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339 <conditional name="db_opts"> |
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340 <param name="db_opts_selector" type="select" label="Subject database/sequences"> |
22
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341 <option value="db" selected="true">Locally installed BLAST database</option> |
11
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342 <option value="histdb">BLAST database from your history</option> |
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343 <option value="file">FASTA file from your history (see warning note below)</option> |
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344 </param> |
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345 <when value="db"> |
20
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346 <param name="database" type="select" multiple="true" label="Nucleotide 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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347 <options from_data_table="blastdb" /> |
11
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348 </param> |
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349 <param name="histdb" type="hidden" value="" /> |
22
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350 <param name="subject" type="hidden" value="" /> |
11
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351 </when> |
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352 <when value="histdb"> |
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353 <param name="database" type="hidden" value="" /> |
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|
354 <param name="histdb" type="data" format="blastdbn" label="Nucleotide BLAST database" /> |
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355 <param name="subject" type="hidden" value="" /> |
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356 </when> |
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357 <when value="file"> |
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358 <param name="database" type="hidden" value="" /> |
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359 <param name="histdb" type="hidden" value="" /> |
23 | 360 <param argument="-subject" type="data" format="fasta,fasta.gz" label="Nucleotide FASTA subject file to use instead of a database"/> |
11
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361 </when> |
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|
362 </conditional> |
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|
363 </xml> |
23 | 364 |
11
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|
365 <xml name="input_conditional_protein_db"> |
22
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366 <!-- Usually database argument mapped to -db, but -in in segmasker --> |
11
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367 <conditional name="db_opts"> |
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368 <param name="db_opts_selector" type="select" label="Subject database/sequences"> |
22
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369 <option value="db" selected="true">Locally installed BLAST database</option> |
11
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|
370 <option value="histdb">BLAST database from your history</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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|
371 <option value="file">FASTA file from your history (see warning note below)</option> |
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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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|
372 </param> |
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|
373 <when value="db"> |
20
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Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
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|
374 <param name="database" type="select" multiple="true" 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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14
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375 <options from_data_table="blastdb_p" /> |
11
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376 </param> |
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|
377 <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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|
378 <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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|
379 </when> |
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|
380 <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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|
381 <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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parents:
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|
382 <param name="histdb" type="data" format="blastdbp" label="Protein BLAST database" /> |
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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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|
383 <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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parents:
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|
384 </when> |
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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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|
385 <when value="file"> |
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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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|
386 <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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parents:
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|
387 <param name="histdb" type="hidden" value="" /> |
22
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388 <param argument="-subject" type="data" format="fasta" label="Protein FASTA subject file to use instead of a database"/> |
11
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389 </when> |
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|
390 </conditional> |
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parents:
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|
391 </xml> |
23 | 392 |
11
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393 <xml name="input_conditional_pssm"> |
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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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394 <conditional name="db_opts"> |
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parents:
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|
395 <param name="db_opts_selector" type="select" label="Protein domain database (PSSM)"> |
22
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396 <option value="db" selected="true">Locally installed BLAST protein domain database</option> |
11
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peterjc
parents:
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|
397 <option value="histdb">BLAST protein domain database from your history</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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|
398 </param> |
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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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|
399 <when value="db"> |
22
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21
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|
400 <param name="database" argument="-db" type="select" label="Protein domain database"> |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
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|
401 <options from_data_table="blastdb_d" /> |
11
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|
402 </param> |
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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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|
403 <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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parents:
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|
404 <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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|
405 </when> |
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parents:
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|
406 <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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parents:
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|
407 <param name="database" type="hidden" value="" /> |
22
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21
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|
408 <param name="histdb" argument="-db" type="data" format="blastdbd" label="Protein domain database" /> |
11
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|
409 <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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parents:
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|
410 </when> |
4c4a0da938ff
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parents:
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|
411 </conditional> |
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|
412 </xml> |
23 | 413 |
11
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parents:
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|
414 <xml name="input_conditional_choose_db_type"> |
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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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|
415 <conditional name="db_opts"> |
22
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416 <param argument="-db_type" type="select" label="Type of BLAST database"> |
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|
417 <option value="nucl" selected="true">Nucleotide</option> |
11
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418 <option value="prot">Protein</option> |
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419 </param> |
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parents:
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|
420 <when value="nucl"> |
22
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parents:
21
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|
421 <param name="database" argument="-db" type="select" multiple="true" label="Nucleotide BLAST database"> |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
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|
422 <options from_data_table="blastdb" /> |
11
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parents:
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|
423 </param> |
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parents:
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|
424 </when> |
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425 <when value="prot"> |
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426 <param name="database" argument="-db" type="select" multiple="true" label="Protein BLAST database"> |
15
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427 <options from_data_table="blastdb_p" /> |
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428 </param> |
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429 </when> |
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430 </conditional> |
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431 </xml> |
23 | 432 |
11
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433 <xml name="input_parse_deflines"> |
22
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434 <param argument="-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"/> |
11
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435 </xml> |
23 | 436 |
11
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437 <xml name="input_filter_query_default_false"> |
22
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438 <param name="filter_query" argument="-seg" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" /> |
11
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439 </xml> |
23 | 440 |
11
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441 <xml name="input_filter_query_default_true"> |
22
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442 <param name="filter_query" argument="-seg" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> |
11
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443 </xml> |
23 | 444 |
11
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445 <xml name="input_max_hits"> |
22
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446 <param name="max_hits" type="integer" min="0" value="0" label="Maximum hits to show" help="Use zero for default limits" /> |
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447 <param argument="-max_hsps" type="integer" min="1" optional="true" value="" label="Maximum number of HSPs (alignments) to keep for any single query-subject pair" help="The HSPs shown will be the best as judged by expect value. If this option is not set, BLAST shows all HSPs meeting the expect value criteria" /> |
11
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448 </xml> |
23 | 449 |
11
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450 <xml name="input_evalue"> |
22
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451 <param name="evalue_cutoff" argument="-evalue" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> |
11
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452 </xml> |
23 | 453 |
11
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454 <xml name="input_word_size"> |
23 | 455 <param argument="-word_size" type="integer" min="2" optional="true" |
456 label="Word size for wordfinder algorithm" | |
457 help="Leave blank for default, otherwise minimum 2" /> | |
11
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458 </xml> |
23 | 459 |
11
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460 <xml name="input_strand"> |
22
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461 <param argument="-strand" type="select" label="Query strand(s) to search against database/subject"> |
11
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462 <option value="-strand both">Both</option> |
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463 <option value="-strand plus">Plus (forward)</option> |
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464 <option value="-strand minus">Minus (reverse complement)</option> |
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465 </param> |
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466 </xml> |
23 | 467 |
15
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468 <xml name="input_qcov_hsp_perc"> |
22
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469 <param argument="-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 qcovhsp"/> |
11
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470 </xml> |
23 | 471 |
472 <xml name="input_window_size"> | |
473 <param argument="-window_size" type="integer" optional="true" min="0" | |
474 label="Multiple hits window size: use 0 to specify 1-hit algorithm, leave blank for default" | |
475 help="Default window size varies with substitution matrix and BLAST type. Enter an integer to override the default."/> | |
476 </xml> | |
477 | |
478 <xml name="input_threshold"> | |
479 <param argument="-threshold" type="integer" optional="true" min="0" | |
480 label="Minimum score to add a word to the BLAST lookup table." | |
481 help="Leave blank for default, which varies based on application."/> | |
482 </xml> | |
483 | |
484 <xml name="input_comp_based_stats"> | |
485 <param argument="-comp_based_stats" type="select" | |
486 label="Composition-based statistics" | |
487 help="The default value varies based on application and task. Most common default is 2."> | |
488 <option value="">Use default</option> | |
489 <option value="0">0: No composition-based statistics</option> | |
490 <option value="1">1: Composition-based statistics as in NAR 29:2994-3005, 2001</option> | |
491 <option value="2">2: Composition-based score adjustment as in Bioinformatics | |
492 21:902-911, 2005, conditioned on sequence properties</option> | |
493 <option value="3">3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally</option> | |
494 </param> | |
495 </xml> | |
496 | |
11
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497 <xml name="advanced_options"> |
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498 <conditional name="adv_opts"> |
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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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499 <param name="adv_opts_selector" type="select" label="Advanced Options"> |
22
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500 <option value="basic" selected="true">Hide Advanced Options</option> |
11
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501 <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.
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502 </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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503 <when value="basic" /> |
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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504 <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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505 <yield /> |
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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506 </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.
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507 </conditional> |
11
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508 </xml> |
23 | 509 |
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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510 <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.
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511 <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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512 <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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513 label="Restrict search of database to a given set of ID's" |
22
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514 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."> |
6f386c5dc4fb
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515 <option value="none" selected="true">No restriction, search the entire database</option> |
15
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516 <option value="gilist">GI identifiers</option> |
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517 <option value="negative_gilist">Negative GI identifiers</option> |
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Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
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518 <option value="seqidlist">Sequence identifiers (SeqId's)</option> |
14
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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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519 </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
parents:
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520 <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
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521 <when value="gilist"> |
22
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522 <param argument="-gilist" type="data" format="txt" label="Restrict search of database to GI's listed in this file" |
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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523 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
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524 </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
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525 <when value="negative_gilist"> |
22
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526 <param argument="-negative_gilist" type="data" format="txt" label="Restrict search of database to everything except the GI's listed in this file" |
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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527 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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528 </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
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529 <when value="seqidlist"> |
22
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530 <param argument="-seqidlist" type="data" format="txt" label=" Restrict search of database to list of SeqId's" |
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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|
531 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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532 </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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533 </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
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534 </xml> |
23 | 535 <!--Tokens--> |
536 <token name="@ADV_MATRIX_GAPCOSTS@"><![CDATA[ | |
537 #if str($adv_opts.matrix_gapcosts.matrix): | |
538 -matrix '${adv_opts.matrix_gapcosts.matrix}' | |
539 ${adv_opts.matrix_gapcosts.gap_costs} | |
15
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Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
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540 #end if |
23 | 541 ]]></token> |
542 | |
543 <token name="@ADV_QCOV_HSP_PERC@"><![CDATA[ | |
544 #if float(str($adv_opts.qcov_hsp_perc)) > 0: | |
545 -qcov_hsp_perc '${adv_opts.qcov_hsp_perc}' | |
546 #end if | |
547 ]]></token> | |
548 | |
549 <token name="@ADV_ID_LIST_FILTER@"><![CDATA[ | |
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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.
peterjc
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550 #if $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'negative_gilist': |
23 | 551 -negative_gilist '${adv_opts.adv_optional_id_files_opts.negative_gilist}' |
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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552 #elif $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'gilist': |
23 | 553 -gilist '{$adv_opts.adv_optional_id_files_opts.gilist}' |
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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554 #elif $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'seqidlist': |
23 | 555 -seqidlist '${adv_opts.adv_optional_id_files_opts.seqidlist}' |
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556 #end if |
23 | 557 ]]></token> |
558 | |
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559 <token name="@THREADS@">-num_threads "\${GALAXY_SLOTS:-8}"</token> |
23 | 560 |
561 <token name="@BLAST_DB_SUBJECT@"><![CDATA[ | |
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562 #if $db_opts.db_opts_selector == "db": |
22
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563 -db '${" ".join(str($db_opts.database.fields.path).split(","))}' |
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564 #elif $db_opts.db_opts_selector == "histdb": |
22
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565 -db '${os.path.join($db_opts.histdb.extra_files_path, "blastdb")}' |
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566 #else: |
23 | 567 #if $db_opts.subject.is_of_type('fasta.gz'): |
568 -subject <(gunzip -c '${$db_opts.subject}') | |
569 #else: | |
570 -subject '${db_opts.subject}' | |
571 #end if | |
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572 #end if |
23 | 573 ]]></token> |
574 | |
575 <token name="@BLAST_OUTPUT@"><![CDATA[ -out '$output1' | |
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576 ##Set the extended list here so when we add things, saved workflows are not affected |
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577 #if str($output.out_format)=="ext": |
22
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578 -outfmt '6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen salltitles' |
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579 #elif str($output.out_format)=="cols" |
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580 ##Pick your own columns. Galaxy gives us it comma separated, BLAST+ wants space separated: |
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581 ##TODO - Can we catch the user picking no columns and raise an error here? |
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582 #set cols = (str($output.std_cols)+","+str($output.ext_cols)+","+str($output.ids_cols)+","+str($output.misc_cols)+","+str($output.tax_cols)).replace("None", "").replace(",,", ",").replace(",", " ").strip() |
22
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583 -outfmt '6 $cols' |
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584 #else: |
22
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585 ## Note do not quote this as can be '0 -html' which is really two arguments |
23 | 586 -outfmt ${output.out_format} |
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587 #end if |
23 | 588 ]]></token> |
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589 <token name="@ADV_FILTER_QUERY@">$adv_opts.filter_query</token> |
23 | 590 <token name="@ADV_MAX_HITS@"><![CDATA[ |
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591 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string |
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592 ## Note -max_target_seqs used to simply override -num_descriptions and -num_alignments |
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593 ## but this was changed in BLAST+ 2.2.27 onwards to force their use (raised with NCBI) |
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594 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): |
22
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595 #if str($output.out_format) in ["6", "ext", "cols", "5"]: |
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596 ## Most output formats use this, including tabular and XML: |
23 | 597 -max_target_seqs '${adv_opts.max_hits}' |
22
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598 #else |
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599 ## Text and HTML output formats 0-4 currently need this instead: |
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600 -num_descriptions $adv_opts.max_hits -num_alignments $adv_opts.max_hits |
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601 #end if |
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602 #end if |
22
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603 #if str($adv_opts.max_hsps) |
23 | 604 -max_hsps '${adv_opts.max_hsps}' |
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605 #end if |
23 | 606 ]]></token> |
607 <token name="@ADV_WORD_SIZE@"><![CDATA[ | |
608 #if str($adv_opts.word_size): | |
609 -word_size '${adv_opts.word_size}' | |
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610 #end if |
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611 $adv_opts.parse_deflines |
23 | 612 ]]></token> |
613 <token name="@ADV_WINDOW_SIZE@"><![CDATA[ | |
614 #if str($adv_opts.window_size): | |
615 -window_size '${adv_opts.window_size}' | |
616 #end if | |
617 ]]></token> | |
618 | |
619 <token name="@ADV_THRESHOLD@"><![CDATA[ | |
620 #if str($adv_opts.threshold): | |
621 -threshold '${adv_opts.threshold}' | |
622 #end if | |
623 ]]></token> | |
624 | |
625 <token name="@ADV_COMP_BASED_STATS@"><![CDATA[ | |
626 #if str($adv_opts.comp_based_stats): | |
627 -comp_based_stats '${adv_opts.comp_based_stats}' | |
628 #end if | |
629 ]]></token> | |
630 | |
631 <token name="@ADV_GAPOPEN@"><![CDATA[ | |
632 #if str($adv_opts.gapopen): | |
633 -gapopen '${adv_opts.gapopen}' | |
634 #end if | |
635 ]]></token> | |
636 | |
637 <token name="@ADV_GAPEXTEND@"><![CDATA[ | |
638 #if str($adv_opts.gapextend): | |
639 -gapextend '${adv_opts.gapextend}' | |
640 #end if | |
641 ]]></token> | |
642 | |
643 <token name="@ADV_MATRIX@"><![CDATA[ | |
644 #if str($adv_opts.matrix): | |
645 -matrix '${adv_opts.matrix}' | |
646 #end if | |
647 ]]></token> | |
648 | |
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649 <!-- @ON_DB_SUBJECT@ is for use with @BLAST_DB_SUBJECT@ --> |
23 | 650 <token name="@ON_DB_SUBJECT@"><![CDATA[ |
651 #if str($db_opts.db_opts_selector)=='db' | |
22
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652 '${db_opts.database}' |
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653 #elif str($db_opts.db_opts_selector)=='histdb' |
22
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654 '${db_opts.histdb.name}' |
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655 #else |
22
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656 '${db_opts.subject.name}' |
23 | 657 #end if |
658 ]]></token> | |
659 | |
660 <token name="@REFERENCES@"><![CDATA[ | |
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661 Peter J. A. Cock, John M. Chilton, Björn GrĂ¼ning, James E. Johnson, Nicola Soranzo (2015). |
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662 NCBI BLAST+ integrated into Galaxy. *GigaScience* 4:39 |
23 | 663 https://doi.org/10.1186/s13742-015-0080-7 |
11
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664 |
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665 Christiam Camacho et al. (2009). |
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666 BLAST+: architecture and applications. |
17
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667 *BMC Bioinformatics* 15;10:421. |
23 | 668 https://doi.org/10.1186/1471-2105-10-421 |
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669 |
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670 This wrapper is available to install into other Galaxy Instances via the Galaxy |
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671 Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus |
23 | 672 ]]></token> |
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673 <xml name="blast_citations"> |
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674 <citations> |
23 | 675 <citation type="doi">10.1093/nar/25.17.3389</citation> |
14
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676 <citation type="doi">10.1186/1471-2105-10-421</citation> |
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677 <citation type="doi">10.1186/s13742-015-0080-7</citation> |
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678 </citations> |
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679 </xml> |
23 | 680 <token name="@OUTPUT_FORMAT@"><![CDATA[ |
681 **Output format** | |
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682 |
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683 Because Galaxy focuses on processing tabular data, the default output of this |
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684 tool is tabular. The standard BLAST+ tabular output contains 12 columns: |
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685 |
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686 ====== ========= ============================================ |
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687 Column NCBI name Description |
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688 ------ --------- -------------------------------------------- |
23 | 689 1 qaccver Query accession dot version |
690 2 saccver Subject accession dot version (database hit) | |
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691 3 pident Percentage of identical matches |
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692 4 length Alignment length |
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693 5 mismatch Number of mismatches |
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694 6 gapopen Number of gap openings |
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695 7 qstart Start of alignment in query |
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696 8 qend End of alignment in query |
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697 9 sstart Start of alignment in subject (database hit) |
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698 10 send End of alignment in subject (database hit) |
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699 11 evalue Expectation value (E-value) |
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700 12 bitscore Bit score |
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701 ====== ========= ============================================ |
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702 |
23 | 703 Until BLAST+ 2.5.0, the first two columns were ``qseqid`` and ``sseqid``, |
704 which were usually strings contained multiple pipe-separated entries. | |
705 In BLAST+ 2.5.0, the first two columns became ``qacc`` and ``sacc`` | |
706 (accesion only), while in BLAST+ 2.6.0 this was changed again to use | |
707 ``qaccver`` and ``saccver`` (accession dot version). | |
708 | |
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709 The BLAST+ tools can optionally output additional columns of information, |
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710 but this takes longer to calculate. Many commonly used extra columns are |
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711 included by selecting the extended tabular output. The extra columns are |
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712 included *after* the standard 12 columns. This is so that you can write |
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713 workflow filtering steps that accept either the 12 or 25 column tabular |
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714 BLAST output. Galaxy now uses this extended 25 column output by default. |
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715 |
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716 ====== ============= =========================================== |
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717 Column NCBI name Description |
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718 ------ ------------- ------------------------------------------- |
13
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719 13 sallseqid All subject Seq-id(s), separated by a ';' |
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720 14 score Raw score |
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721 15 nident Number of identical matches |
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722 16 positive Number of positive-scoring matches |
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723 17 gaps Total number of gaps |
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724 18 ppos Percentage of positive-scoring matches |
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725 19 qframe Query frame |
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726 20 sframe Subject frame |
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727 21 qseq Aligned part of query sequence |
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728 22 sseq Aligned part of subject sequence |
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729 23 qlen Query sequence length |
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730 24 slen Subject sequence length |
23 | 731 25 salltitles All subject title(s), separated by a '<>' |
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732 ====== ============= =========================================== |
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733 |
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734 The third option is to customise the tabular output by selecting which |
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735 columns you want, from the standard set of 12, the default set of 25, |
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736 or any of the additional columns BLAST+ offers (including species name). |
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737 |
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738 The fourth option is BLAST XML output, which is designed to be parsed by |
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739 another program, and is understood by some Galaxy tools. |
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740 |
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741 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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742 The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. |
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743 The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. |
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744 The two query anchored outputs show a multiple sequence alignment between the query and all the matches, |
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745 and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). |
23 | 746 ]]></token> |
747 <token name="@FASTA_WARNING@"><![CDATA[ | |
748 .. class:: warningmark | |
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749 |
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750 You can also search against a FASTA file of subject (target) |
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751 sequences. This is *not* advised because it is slower (only one |
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752 CPU is used), but more importantly gives e-values for pairwise |
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753 searches (very small e-values which will look overly signficiant). |
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754 In most cases you should instead turn the other FASTA file into a |
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755 database first using *makeblastdb* and search against that. |
23 | 756 ]]></token> |
757 <token name="@SEARCH_TIME_WARNING@"><![CDATA[ | |
758 .. class:: warningmark | |
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759 |
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760 **Note**. Database searches may take a substantial amount of time. |
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761 For large input datasets it is advisable to allow overnight processing. |
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762 |
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763 ----- |
23 | 764 ]]></token> |
765 <token name="@CLI_OPTIONS@"><![CDATA[ | |
766 **Advanced Options** | |
767 | |
768 For help with advanced options and their default values, visit the | |
769 NCBI BLAST® Command Line Applications User Manual, Appendices, | |
770 `Options for the command-line applications | |
771 <https://www.ncbi.nlm.nih.gov/books/NBK279684/#_appendices_Options_for_the_commandline_a_>`_. | |
772 | |
773 For amino acid substitution matrices, see `BLAST Substitution Matrices | |
774 <https://www.ncbi.nlm.nih.gov/books/NBK279684/#_appendices_BLAST_Substitution_Matrices_>`_ in the same | |
775 appendices. | |
776 | |
777 ]]></token> | |
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778 </macros> |