Mercurial > repos > devteam > ncbi_blast_plus
annotate tools/ncbi_blast_plus/ncbi_macros.xml @ 27:6f8ea4b9a2c4 draft
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
author | peterjc |
---|---|
date | Wed, 09 Sep 2020 15:32:17 +0000 |
parents | 2889433c7ae1 |
children | 87a7ee4cb36f |
rev | line source |
---|---|
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
changeset
|
1 <macros> |
27
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
2 <token name="@TOOL_VERSION@">2.7.1</token> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
3 <token name="@VERSION_SUFFIX@">0</token> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
4 <token name="@PROFILE@">16.10</token> |
17
697f40151eaf
v0.1.05 - Update citation information now GigaScience paper is out
peterjc
parents:
16
diff
changeset
|
5 <xml name="parallelism"> |
697f40151eaf
v0.1.05 - Update citation information now GigaScience paper is out
peterjc
parents:
16
diff
changeset
|
6 <!-- If job splitting is enabled, break up the query file into parts --> |
697f40151eaf
v0.1.05 - Update citation information now GigaScience paper is out
peterjc
parents:
16
diff
changeset
|
7 <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1" /> |
697f40151eaf
v0.1.05 - Update citation information now GigaScience paper is out
peterjc
parents:
16
diff
changeset
|
8 </xml> |
23 | 9 |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
10 <xml name="preamble"> |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
11 <requirements> |
27
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
12 <requirement type="package" version="@TOOL_VERSION@">blast</requirement> |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
13 </requirements> |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
14 <version_command>@BINARY@ -version</version_command> |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
15 </xml> |
23 | 16 |
25 | 17 <xml name="nucl_query"> |
18 <param argument="-query" type="data" format="fasta,fasta.gz" label="Nucleotide query sequence(s)"/> | |
19 </xml> | |
20 | |
21 <xml name="prot_query"> | |
22 <param argument="-query" type="data" format="fasta,fasta.gz" label="Protein query sequence(s)"/> | |
23 </xml> | |
24 | |
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
changeset
|
25 <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
parents:
diff
changeset
|
26 <change_format> |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
27 <when input="output.out_format" value="0" format="txt"/> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
28 <when input="output.out_format" value="0 -html" format="html"/> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
29 <when input="output.out_format" value="2" format="txt"/> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
30 <when input="output.out_format" value="2 -html" format="html"/> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
31 <when input="output.out_format" value="4" format="txt"/> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
32 <when input="output.out_format" value="4 -html" format="html"/> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
33 <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
changeset
|
34 </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
changeset
|
35 </xml> |
23 | 36 |
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
changeset
|
37 <xml name="input_out_format"> |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
38 <conditional name="output"> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
39 <param name="out_format" argument="-outfmt" type="select" label="Output format"> |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
40 <option value="6">Tabular (standard 12 columns)</option> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
41 <option value="ext" selected="true">Tabular (extended 25 columns)</option> |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
42 <option value="cols">Tabular (select which columns)</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
43 <option value="5">BLAST XML</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
44 <option value="0">Pairwise text</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
45 <option value="0 -html">Pairwise HTML</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
46 <option value="2">Query-anchored text</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
47 <option value="2 -html">Query-anchored HTML</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
48 <option value="4">Flat query-anchored text</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
49 <option value="4 -html">Flat query-anchored HTML</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
50 <!-- |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
51 <option value="-outfmt 11">BLAST archive format (ASN.1)</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
52 --> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
53 </param> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
54 <when value="6"/> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
55 <when value="ext"/> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
56 <when value="cols"> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
57 <param name="std_cols" type="select" multiple="true" display="checkboxes" label="Standard columns"> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
58 <option selected="true" value="qseqid">qseqid = Query Seq-id (ID of your sequence)</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
59 <option selected="true" value="sseqid">sseqid = Subject Seq-id (ID of the database hit)</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
60 <option selected="true" value="pident">pident = Percentage of identical matches</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
61 <option selected="true" value="length">length = Alignment length</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
62 <option selected="true" value="mismatch">mismatch = Number of mismatches</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
63 <option selected="true" value="gapopen">gapopen = Number of gap openings</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
64 <option selected="true" value="qstart">qstart = Start of alignment in query</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
65 <option selected="true" value="qend">qend = End of alignment in query</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
66 <option selected="true" value="sstart">sstart = Start of alignment in subject (database hit)</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
67 <option selected="true" value="send">send = End of alignment in subject (database hit)</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
68 <option selected="true" value="evalue">evalue = Expectation value (E-value)</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
69 <option selected="true" value="bitscore">bitscore = Bit score</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
70 </param> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
71 <param name="ext_cols" type="select" multiple="true" display="checkboxes" label="Extended columns"> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
72 <option value="sallseqid">sallseqid = All subject Seq-id(s), separated by a ';'</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
73 <option value="score">score = Raw score</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
74 <option value="nident">nident = Number of identical matches</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
75 <option value="positive">positive = Number of positive-scoring matches</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
76 <option value="gaps">gaps = Total number of gaps</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
77 <option value="ppos">ppos = Percentage of positive-scoring matches</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
78 <option value="qframe">qframe = Query frame</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
79 <option value="sframe">sframe = Subject frame</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
80 <option value="qseq">qseq = Aligned part of query sequence</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
81 <option value="sseq">sseq = Aligned part of subject sequence</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
82 <option value="qlen">qlen = Query sequence length</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
83 <option value="slen">slen = Subject sequence length</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
84 <option value="salltitles">salltitles = All subject title(s), separated by a '<>'</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
85 </param> |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
86 <param name="ids_cols" type="select" multiple="true" display="checkboxes" label="Other identifier columns"> |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
87 <option value="qgi">qgi = Query GI</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
88 <option value="qacc">qacc = Query accesion</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
89 <option value="qaccver">qaccver = Query accesion.version</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
90 <option value="sallseqid">sallseqid = All subject Seq-id(s), separated by a ';'</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
91 <option value="sgi">sgi = Subject GI</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
92 <option value="sallgi">sallgi = All subject GIs</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
93 <option value="sacc">sacc = Subject accession</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
94 <option value="saccver">saccver = Subject accession.version</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
95 <option value="sallacc">sallacc = All subject accessions</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
96 <option value="stitle">stitle = Subject Title</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
97 </param> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
98 <param name="misc_cols" type="select" multiple="true" display="checkboxes" label="Miscellaneous columns"> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
99 <option value="sstrand">sstrand = Subject Strand</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
100 <!-- Is it really worth including 'frames' given have 'qframe' and 'sframe'? --> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
101 <option value="frames">frames = Query and subject frames separated by a '/'</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
102 <option value="btop">btop = Blast traceback operations (BTOP)</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
103 <option value="qcovs">qcovs = Query Coverage Per Subject</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
104 <option value="qcovhsp">qcovhsp = Query Coverage Per HSP</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
105 </param> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
106 <param name="tax_cols" type="select" multiple="true" display="checkboxes" label="Taxonomy columns"> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
107 <option value="staxids">staxids = unique Subject Taxonomy ID(s), separated by a ';' (in numerical order)</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
108 <!-- TODO, how to handle the taxonomy data file dependency? If missing these give N/A --> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
109 <option value="sscinames">sscinames = unique Subject Scientific Name(s), separated by a ';'</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
110 <option value="scomnames">scomnames = unique Subject Common Name(s), separated by a ';'</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
111 <option value="sblastnames">sblastnames = unique Subject Blast Name(s), separated by a ';' (in alphabetical order)</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
112 <option value="sskingdoms">sskingdoms = unique Subject Super Kingdom(s), separated by a ';' (in alphabetical order)</option> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
113 </param> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
114 </when> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
115 <when value="5"/> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
116 <when value="0"/> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
117 <when value="0 -html"/> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
118 <when value="2"/> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
119 <when value="2 -html"/> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
120 <when value="4"/> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
121 <when value="4 -html"/> |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
122 </conditional> |
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
changeset
|
123 </xml> |
23 | 124 |
125 <xml name="input_matrix_gapcosts"> | |
126 <conditional name="matrix_gapcosts"> | |
127 <param argument="-matrix" type="select" label="Scoring matrix and gap costs"> | |
128 <option value="" selected="true">Use Defaults</option> | |
129 <option value="BLOSUM90">BLOSUM90</option> | |
130 <option value="BLOSUM80">BLOSUM80</option> | |
131 <option value="BLOSUM62">BLOSUM62</option> | |
132 <option value="BLOSUM50">BLOSUM50</option> | |
133 <option value="BLOSUM45">BLOSUM45</option> | |
134 <option value="PAM250">PAM250</option> | |
135 <option value="PAM70">PAM70</option> | |
136 <option value="PAM30">PAM30</option> | |
137 </param> | |
138 <when value=""> | |
139 <!-- do nothing --> | |
140 </when> | |
141 <when value="BLOSUM90"> | |
142 <param name="gap_costs" type="select" label="Gap Costs"> | |
143 <option value="" selected="true">Use defaults</option> | |
144 <option value="-gapopen 9 -gapextend 2">Existence: 9 Extension: 2</option> | |
145 <option value="-gapopen 8 -gapextend 2">Existence: 8 Extension: 2</option> | |
146 <option value="-gapopen 7 -gapextend 2">Existence: 7 Extension: 2</option> | |
147 <option value="-gapopen 6 -gapextend 2">Existence: 6 Extension: 2</option> | |
148 <option value="-gapopen 11 -gapextend 1">Existence: 11 Extension: 1</option> | |
149 <option value="-gapopen 10 -gapextend 1">Existence: 10 Extension: 1</option> | |
150 <option value="-gapopen 9 -gapextend 1">Existence: 9 Extension: 1</option> | |
151 </param> | |
152 | |
153 </when> | |
154 <when value="BLOSUM80"> | |
155 <param name="gap_costs" type="select" label="Gap Costs"> | |
156 <option value="" selected="true">Use defaults</option> | |
157 <option value="-gapopen 8 -gapextend 2">Existence: 8 Extension: 2</option> | |
158 <option value="-gapopen 7 -gapextend 2">Existence: 7 Extension: 2</option> | |
159 <option value="-gapopen 6 -gapextend 2">Existence: 6 Extension: 2</option> | |
160 <option value="-gapopen 11 -gapextend 1">Existence: 11 Extension: 1</option> | |
161 <option value="-gapopen 10 -gapextend 1">Existence: 10 Extension: 1</option> | |
162 <option value="-gapopen 9 -gapextend 1">Existence: 9 Extension: 1</option> | |
163 </param> | |
164 </when> | |
165 <when value="BLOSUM62"> | |
166 <param name="gap_costs" type="select" label="Gap Costs"> | |
167 <option value="" selected="true">Use defaults</option> | |
168 <option value="-gapopen 11 -gapextend 2">Existence: 11 Extension: 2</option> | |
169 <option value="-gapopen 10 -gapextend 2">Existence: 10 Extension: 2</option> | |
170 <option value="-gapopen 9 -gapextend 2">Existence: 9 Extension: 2</option> | |
171 <option value="-gapopen 8 -gapextend 2">Existence: 8 Extension: 2</option> | |
172 <option value="-gapopen 7 -gapextend 2">Existence: 7 Extension: 2</option> | |
173 <option value="-gapopen 6 -gapextend 2">Existence: 6 Extension: 2</option> | |
174 <option value="-gapopen 13 -gapextend 1">Existence: 13 Extension: 1</option> | |
175 <option value="-gapopen 12 -gapextend 1">Existence: 12 Extension: 1</option> | |
176 <option value="-gapopen 11 -gapextend 1">Existence: 11 Extension: 1</option> | |
177 <option value="-gapopen 10 -gapextend 1">Existence: 10 Extension: 1</option> | |
178 <option value="-gapopen 9 -gapextend 1">Existence: 9 Extension: 1</option> | |
179 </param> | |
180 | |
181 </when> | |
182 <when value="BLOSUM50"> | |
183 <param name="gap_costs" type="select" label="Gap Costs"> | |
184 <option value="" selected="true">Use defaults</option> | |
185 <option value="-gapopen 13 -gapextend 3">Existence: 13 Extension: 3</option> | |
186 <option value="-gapopen 12 -gapextend 3">Existence: 12 Extension: 3</option> | |
187 <option value="-gapopen 11 -gapextend 3">Existence: 11 Extension: 3</option> | |
188 <option value="-gapopen 10 -gapextend 3">Existence: 10 Extension: 3</option> | |
189 <option value="-gapopen 9 -gapextend 3">Existence: 9 Extension: 3</option> | |
190 <option value="-gapopen 16 -gapextend 2">Existence: 16 Extension: 2</option> | |
191 <option value="-gapopen 15 -gapextend 2">Existence: 15 Extension: 2</option> | |
192 <option value="-gapopen 14 -gapextend 2">Existence: 14 Extension: 2</option> | |
193 <option value="-gapopen 13 -gapextend 2">Existence: 13 Extension: 2</option> | |
194 <option value="-gapopen 12 -gapextend 2">Existence: 12 Extension: 2</option> | |
195 <option value="-gapopen 19 -gapextend 1">Existence: 19 Extension: 1</option> | |
196 <option value="-gapopen 18 -gapextend 1">Existence: 18 Extension: 1</option> | |
197 <option value="-gapopen 17 -gapextend 1">Existence: 17 Extension: 1</option> | |
198 <option value="-gapopen 16 -gapextend 1">Existence: 16 Extension: 1</option> | |
199 <option value="-gapopen 15 -gapextend 1">Existence: 15 Extension: 1</option> | |
200 </param> | |
201 | |
202 </when> | |
203 <when value="BLOSUM45"> | |
204 <param name="gap_costs" type="select" label="Gap Costs"> | |
205 <option value="" selected="true">Use defaults</option> | |
206 <option value="-gapopen 13 -gapextend 3">Existence: 13 Extension: 3</option> | |
207 <option value="-gapopen 12 -gapextend 3">Existence: 12 Extension: 3</option> | |
208 <option value="-gapopen 11 -gapextend 3">Existence: 11 Extension: 3</option> | |
209 <option value="-gapopen 10 -gapextend 3">Existence: 10 Extension: 3</option> | |
210 <option value="-gapopen 15 -gapextend 2">Existence: 15 Extension: 2</option> | |
211 <option value="-gapopen 14 -gapextend 2">Existence: 14 Extension: 2</option> | |
212 <option value="-gapopen 13 -gapextend 2">Existence: 13 Extension: 2</option> | |
213 <option value="-gapopen 12 -gapextend 2">Existence: 12 Extension: 2</option> | |
214 <option value="-gapopen 19 -gapextend 1">Existence: 19 Extension: 1</option> | |
215 <option value="-gapopen 18 -gapextend 1">Existence: 18 Extension: 1</option> | |
216 <option value="-gapopen 17 -gapextend 1">Existence: 17 Extension: 1</option> | |
217 <option value="-gapopen 16 -gapextend 1">Existence: 16 Extension: 1</option> | |
218 </param> | |
219 </when> | |
220 <when value="PAM250"> | |
221 <param name="gap_costs" type="select" label="Gap Costs"> | |
222 <option value="" selected="true">Use defaults</option> | |
223 <option value="-gapopen 15 -gapextend 3">Existence: 15 Extension: 3</option> | |
224 <option value="-gapopen 14 -gapextend 3">Existence: 14 Extension: 3</option> | |
225 <option value="-gapopen 13 -gapextend 3">Existence: 13 Extension: 3</option> | |
226 <option value="-gapopen 12 -gapextend 3">Existence: 12 Extension: 3</option> | |
227 <option value="-gapopen 17 -gapextend 2">Existence: 17 Extension: 2</option> | |
228 <option value="-gapopen 16 -gapextend 2">Existence: 16 Extension: 2</option> | |
229 <option value="-gapopen 15 -gapextend 2">Existence: 15 Extension: 2</option> | |
230 <option value="-gapopen 14 -gapextend 2">Existence: 14 Extension: 2</option> | |
231 <option value="-gapopen 13 -gapextend 2">Existence: 13 Extension: 2</option> | |
232 <option value="-gapopen 21 -gapextend 1">Existence: 21 Extension: 1</option> | |
233 <option value="-gapopen 20 -gapextend 1">Existence: 20 Extension: 1</option> | |
234 <option value="-gapopen 19 -gapextend 1">Existence: 19 Extension: 1</option> | |
235 <option value="-gapopen 18 -gapextend 1">Existence: 18 Extension: 1</option> | |
236 <option value="-gapopen 17 -gapextend 1">Existence: 17 Extension: 1</option> | |
237 </param> | |
238 | |
239 </when> | |
240 <when value="PAM70"> | |
241 <param name="gap_costs" type="select" label="Gap Costs"> | |
242 <option value="" selected="true">Use defaults</option> | |
243 <option value="-gapopen 12 -gapextend 3">Existence: 12 Extension: 3</option> | |
244 <option value="-gapopen 11 -gapextend 2">Existence: 11 Extension: 2</option> | |
245 <option value="-gapopen 8 -gapextend 2">Existence: 8 Extension: 2</option> | |
246 <option value="-gapopen 7 -gapextend 2">Existence: 7 Extension: 2</option> | |
247 <option value="-gapopen 6 -gapextend 2">Existence: 6 Extension: 2</option> | |
248 <option value="-gapopen 11 -gapextend 1">Existence: 11 Extension: 1</option> | |
249 <option value="-gapopen 10 -gapextend 1">Existence: 10 Extension: 1</option> | |
250 <option value="-gapopen 9 -gapextend 1">Existence: 9 Extension: 1</option> | |
251 </param> | |
252 | |
253 </when> | |
254 <when value="PAM30"> | |
255 <param name="gap_costs" type="select" label="Gap Costs"> | |
256 <option value="" selected="true">Use defaults</option> | |
257 <option value="-gapopen 15 -gapextend 3">Existence: 15 Extension: 3</option> | |
258 <option value="-gapopen 13 -gapextend 3">Existence: 13 Extension: 3</option> | |
259 <option value="-gapopen 14 -gapextend 2">Existence: 14 Extension: 2</option> | |
260 <option value="-gapopen 7 -gapextend 2">Existence: 7 Extension: 2</option> | |
261 <option value="-gapopen 6 -gapextend 2">Existence: 6 Extension: 2</option> | |
262 <option value="-gapopen 5 -gapextend 2">Existence: 5 Extension: 2</option> | |
263 <option value="-gapopen 14 -gapextend 1">Existence: 14 Extension: 1</option> | |
264 <option value="-gapopen 10 -gapextend 1">Existence: 10 Extension: 1</option> | |
265 <option value="-gapopen 9 -gapextend 1">Existence: 9 Extension: 1</option> | |
266 <option value="-gapopen 8 -gapextend 1">Existence: 8 Extension: 1</option> | |
267 </param> | |
268 </when> | |
269 </conditional> | |
270 </xml> | |
271 <!-- these gapopen and gapextend macros are only used in blastn. | |
272 otherwise, the combined matrix/gapcosts macro is used --> | |
273 <xml name="input_gapopen"> | |
274 <param argument="-gapopen" type="integer" optional="true" min="0" | |
275 label="Cost to open a gap" | |
276 help="Leave blank for default. See tool help for defaults."/> | |
277 </xml> | |
278 | |
279 <xml name="input_gapextend"> | |
280 <param argument="-gapextend" type="integer" optional="true" min="1" | |
281 label="Cost to extend a gap" | |
282 help="Leave blank for default. See tool help for defaults."/> | |
283 </xml> | |
284 | |
285 <!-- this matrix macro is used in deltablast, makeprofiledb, psiblast, and tblastx --> | |
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
changeset
|
286 <xml name="input_scoring_matrix"> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
287 <param argument="-matrix" type="select" label="Scoring matrix"> |
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
changeset
|
288 <option value="BLOSUM90">BLOSUM90</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
changeset
|
289 <option value="BLOSUM80">BLOSUM80</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
changeset
|
290 <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
291 <option value="BLOSUM50">BLOSUM50</option> |
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
changeset
|
292 <option value="BLOSUM45">BLOSUM45</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
changeset
|
293 <option value="PAM250">PAM250</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
changeset
|
294 <option value="PAM70">PAM70</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
changeset
|
295 <option value="PAM30">PAM30</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
changeset
|
296 </param> |
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
changeset
|
297 </xml> |
23 | 298 |
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
changeset
|
299 <xml name="input_query_gencode"> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
300 <param argument="-query_gencode" type="select" label="Query genetic code"> |
23 | 301 <!-- See https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
302 <option value="1" selected="true">1. Standard</option> |
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
changeset
|
303 <option value="2">2. Vertebrate Mitochondrial</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
changeset
|
304 <option value="3">3. Yeast Mitochondrial</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
changeset
|
305 <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</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
changeset
|
306 <option value="5">5. Invertebrate Mitochondrial</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
changeset
|
307 <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</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
changeset
|
308 <option value="9">9. Echinoderm Mitochondrial</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
changeset
|
309 <option value="10">10. Euplotid Nuclear</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
changeset
|
310 <option value="11">11. Bacteria and Archaea</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
changeset
|
311 <option value="12">12. Alternative Yeast Nuclear</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
changeset
|
312 <option value="13">13. Ascidian Mitochondrial</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
changeset
|
313 <option value="14">14. Flatworm Mitochondrial</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
changeset
|
314 <option value="15">15. Blepharisma Macronuclear</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
changeset
|
315 <option value="16">16. Chlorophycean Mitochondrial Code</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
changeset
|
316 <option value="21">21. Trematode Mitochondrial Code</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
changeset
|
317 <option value="22">22. Scenedesmus obliquus mitochondrial Code</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
changeset
|
318 <option value="23">23. Thraustochytrium Mitochondrial Code</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
changeset
|
319 <option value="24">24. Pterobranchia mitochondrial code</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
changeset
|
320 </param> |
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
changeset
|
321 </xml> |
23 | 322 |
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
changeset
|
323 <xml name="input_db_gencode"> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
324 <param argument="-db_gencode" type="select" label="Database/subject genetic code"> |
23 | 325 <!-- See https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details --> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
326 <option value="1" selected="true">1. Standard</option> |
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
changeset
|
327 <option value="2">2. Vertebrate Mitochondrial</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
changeset
|
328 <option value="3">3. Yeast Mitochondrial</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
changeset
|
329 <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</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
changeset
|
330 <option value="5">5. Invertebrate Mitochondrial</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
changeset
|
331 <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</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
changeset
|
332 <option value="9">9. Echinoderm Mitochondrial</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
changeset
|
333 <option value="10">10. Euplotid Nuclear</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
changeset
|
334 <option value="11">11. Bacteria and Archaea</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
changeset
|
335 <option value="12">12. Alternative Yeast Nuclear</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
changeset
|
336 <option value="13">13. Ascidian Mitochondrial</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
changeset
|
337 <option value="14">14. Flatworm Mitochondrial</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
changeset
|
338 <option value="15">15. Blepharisma Macronuclear</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
changeset
|
339 <option value="16">16. Chlorophycean Mitochondrial Code</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
changeset
|
340 <option value="21">21. Trematode Mitochondrial Code</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
changeset
|
341 <option value="22">22. Scenedesmus obliquus mitochondrial Code</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
changeset
|
342 <option value="23">23. Thraustochytrium Mitochondrial Code</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
changeset
|
343 <option value="24">24. Pterobranchia mitochondrial code</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
changeset
|
344 </param> |
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
changeset
|
345 </xml> |
23 | 346 |
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
changeset
|
347 <xml name="input_conditional_nucleotide_db"> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
348 <!-- Usually database argument mapped to -db, but -in in dustmasker --> |
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
changeset
|
349 <conditional name="db_opts"> |
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
changeset
|
350 <param name="db_opts_selector" type="select" label="Subject database/sequences"> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
351 <option value="db" selected="true">Locally installed BLAST database</option> |
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
changeset
|
352 <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.
peterjc
parents:
diff
changeset
|
353 <option value="file">FASTA file from your history (see warning note below)</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
changeset
|
354 </param> |
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
changeset
|
355 <when value="db"> |
20
3034ce97dd33
Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents:
19
diff
changeset
|
356 <param name="database" 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
changeset
|
357 <options from_data_table="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.
peterjc
parents:
diff
changeset
|
358 </param> |
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
changeset
|
359 <param name="histdb" type="hidden" value="" /> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
360 <param name="subject" type="hidden" value="" /> |
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
changeset
|
361 </when> |
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
changeset
|
362 <when value="histdb"> |
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
changeset
|
363 <param name="database" type="hidden" value="" /> |
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
changeset
|
364 <param name="histdb" type="data" format="blastdbn" label="Nucleotide BLAST database" /> |
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
changeset
|
365 <param name="subject" type="hidden" value="" /> |
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
changeset
|
366 </when> |
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
changeset
|
367 <when value="file"> |
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
changeset
|
368 <param name="database" type="hidden" value="" /> |
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
changeset
|
369 <param name="histdb" type="hidden" value="" /> |
23 | 370 <param argument="-subject" type="data" format="fasta,fasta.gz" label="Nucleotide FASTA subject file to use instead of a database"/> |
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
changeset
|
371 </when> |
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
changeset
|
372 </conditional> |
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
changeset
|
373 </xml> |
23 | 374 |
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
changeset
|
375 <xml name="input_conditional_protein_db"> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
376 <!-- Usually database argument mapped to -db, but -in in segmasker --> |
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
changeset
|
377 <conditional name="db_opts"> |
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
changeset
|
378 <param name="db_opts_selector" type="select" label="Subject database/sequences"> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
379 <option value="db" selected="true">Locally installed BLAST database</option> |
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
changeset
|
380 <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.
peterjc
parents:
diff
changeset
|
381 <option value="file">FASTA file from your history (see warning note below)</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
changeset
|
382 </param> |
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
changeset
|
383 <when value="db"> |
20
3034ce97dd33
Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents:
19
diff
changeset
|
384 <param name="database" type="select" multiple="true" label="Protein BLAST database"> |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
385 <options from_data_table="blastdb_p" /> |
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
changeset
|
386 </param> |
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
changeset
|
387 <param name="histdb" type="hidden" value="" /> |
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
changeset
|
388 <param name="subject" type="hidden" value="" /> |
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
changeset
|
389 </when> |
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
changeset
|
390 <when value="histdb"> |
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
changeset
|
391 <param name="database" type="hidden" value="" /> |
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
changeset
|
392 <param name="histdb" type="data" format="blastdbp" label="Protein BLAST database" /> |
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
changeset
|
393 <param name="subject" type="hidden" value="" /> |
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
changeset
|
394 </when> |
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
changeset
|
395 <when value="file"> |
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
changeset
|
396 <param name="database" type="hidden" value="" /> |
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
changeset
|
397 <param name="histdb" type="hidden" value="" /> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
398 <param argument="-subject" type="data" format="fasta" label="Protein FASTA subject file to use instead of a database"/> |
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
changeset
|
399 </when> |
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
changeset
|
400 </conditional> |
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
changeset
|
401 </xml> |
23 | 402 |
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
changeset
|
403 <xml name="input_conditional_pssm"> |
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
changeset
|
404 <conditional name="db_opts"> |
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
changeset
|
405 <param name="db_opts_selector" type="select" label="Protein domain database (PSSM)"> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
406 <option value="db" selected="true">Locally installed BLAST protein domain database</option> |
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
changeset
|
407 <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.
peterjc
parents:
diff
changeset
|
408 </param> |
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
changeset
|
409 <when value="db"> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
410 <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
diff
changeset
|
411 <options from_data_table="blastdb_d" /> |
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
changeset
|
412 </param> |
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
changeset
|
413 <param name="histdb" type="hidden" value="" /> |
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
changeset
|
414 <param name="subject" type="hidden" value="" /> |
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
changeset
|
415 </when> |
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
changeset
|
416 <when value="histdb"> |
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
changeset
|
417 <param name="database" type="hidden" value="" /> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
418 <param name="histdb" argument="-db" type="data" format="blastdbd" label="Protein domain database" /> |
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
changeset
|
419 <param name="subject" type="hidden" value="" /> |
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
changeset
|
420 </when> |
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
changeset
|
421 </conditional> |
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
changeset
|
422 </xml> |
23 | 423 |
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
changeset
|
424 <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.
peterjc
parents:
diff
changeset
|
425 <conditional name="db_opts"> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
426 <param argument="-db_type" type="select" label="Type of BLAST database"> |
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
427 <option value="nucl" selected="true">Nucleotide</option> |
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
changeset
|
428 <option value="prot">Protein</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
changeset
|
429 </param> |
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
changeset
|
430 <when value="nucl"> |
27
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
431 <conditional name="db_origin"> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
432 <param name="db_origin_selector" type="select" label="Subject database/sequences"> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
433 <option value="db" selected="true">Locally installed BLAST database</option> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
434 <option value="histdb">BLAST database from your history</option> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
435 </param> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
436 <when value="db"> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
437 <param name="database" argument="-db" type="select" multiple="true" label="Nucleotide BLAST database"> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
438 <options from_data_table="blastdb" /> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
439 </param> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
440 <param name="histdb" type="hidden" value="" /> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
441 </when> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
442 <when value="histdb"> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
443 <param name="database" type="hidden" value="" /> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
444 <param name="histdb" type="data" format="blastdbn" label="Nucleotide BLAST database" /> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
445 </when> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
446 </conditional> |
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
changeset
|
447 </when> |
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
changeset
|
448 <when value="prot"> |
27
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
449 <conditional name="db_origin"> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
450 <param name="db_origin_selector" type="select" label="Subject database/sequences"> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
451 <option value="db" selected="true">Locally installed BLAST database</option> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
452 <option value="histdb">BLAST database from your history</option> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
453 </param> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
454 <when value="db"> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
455 <param name="database" argument="-db" type="select" multiple="true" label="Protein BLAST database"> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
456 <options from_data_table="blastdb_p" /> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
457 </param> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
458 <param name="histdb" type="hidden" value="" /> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
459 </when> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
460 <when value="histdb"> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
461 <param name="database" type="hidden" value="" /> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
462 <param name="histdb" type="data" format="blastdbp" label="Protein BLAST database" /> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
463 </when> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
464 </conditional> |
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
changeset
|
465 </when> |
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
changeset
|
466 </conditional> |
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
changeset
|
467 </xml> |
23 | 468 |
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
changeset
|
469 <xml name="input_parse_deflines"> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
470 <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
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
changeset
|
471 </xml> |
23 | 472 |
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
changeset
|
473 <xml name="input_filter_query_default_false"> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
474 <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
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
changeset
|
475 </xml> |
23 | 476 |
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
changeset
|
477 <xml name="input_filter_query_default_true"> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
478 <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
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
changeset
|
479 </xml> |
23 | 480 |
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
changeset
|
481 <xml name="input_max_hits"> |
25 | 482 <param name="max_hits" type="integer" min="0" value="0" label="Maximum hits to consider/show" help="Use zero for default limits. For HTML and plain text output this value is passed -num_descriptions and -num_alignments but for XML and tabular etc, this is used with -max_target_seqs instead. In either case, in addition to limiting the final output, this alters internal limits during the search, which can in some cases exclude matches which would otherwise become the best hit." /> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
483 <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
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
changeset
|
484 </xml> |
23 | 485 |
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
changeset
|
486 <xml name="input_evalue"> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
487 <param name="evalue_cutoff" argument="-evalue" type="float" size="15" value="0.001" label="Set expectation value cutoff" /> |
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
changeset
|
488 </xml> |
23 | 489 |
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
changeset
|
490 <xml name="input_word_size"> |
23 | 491 <param argument="-word_size" type="integer" min="2" optional="true" |
492 label="Word size for wordfinder algorithm" | |
493 help="Leave blank for default, otherwise minimum 2" /> | |
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
changeset
|
494 </xml> |
23 | 495 |
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
changeset
|
496 <xml name="input_strand"> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
497 <param argument="-strand" type="select" label="Query strand(s) to search against database/subject"> |
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
changeset
|
498 <option value="-strand both">Both</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
changeset
|
499 <option value="-strand plus">Plus (forward)</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
changeset
|
500 <option value="-strand minus">Minus (reverse complement)</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
changeset
|
501 </param> |
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
changeset
|
502 </xml> |
23 | 503 |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
504 <xml name="input_qcov_hsp_perc"> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
505 <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
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
changeset
|
506 </xml> |
23 | 507 |
508 <xml name="input_window_size"> | |
509 <param argument="-window_size" type="integer" optional="true" min="0" | |
510 label="Multiple hits window size: use 0 to specify 1-hit algorithm, leave blank for default" | |
511 help="Default window size varies with substitution matrix and BLAST type. Enter an integer to override the default."/> | |
512 </xml> | |
513 | |
514 <xml name="input_threshold"> | |
515 <param argument="-threshold" type="integer" optional="true" min="0" | |
516 label="Minimum score to add a word to the BLAST lookup table." | |
517 help="Leave blank for default, which varies based on application."/> | |
518 </xml> | |
519 | |
520 <xml name="input_comp_based_stats"> | |
521 <param argument="-comp_based_stats" type="select" | |
522 label="Composition-based statistics" | |
523 help="The default value varies based on application and task. Most common default is 2."> | |
524 <option value="">Use default</option> | |
525 <option value="0">0: No composition-based statistics</option> | |
526 <option value="1">1: Composition-based statistics as in NAR 29:2994-3005, 2001</option> | |
527 <option value="2">2: Composition-based score adjustment as in Bioinformatics | |
528 21:902-911, 2005, conditioned on sequence properties</option> | |
529 <option value="3">3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally</option> | |
530 </param> | |
531 </xml> | |
532 | |
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
changeset
|
533 <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.
peterjc
parents:
diff
changeset
|
534 <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.
peterjc
parents:
diff
changeset
|
535 <param name="adv_opts_selector" type="select" label="Advanced Options"> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
536 <option value="basic" selected="true">Hide Advanced Options</option> |
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
changeset
|
537 <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
changeset
|
538 </param> |
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
changeset
|
539 <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
parents:
diff
changeset
|
540 <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.
peterjc
parents:
diff
changeset
|
541 <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
parents:
diff
changeset
|
542 </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
parents:
13
diff
changeset
|
543 </conditional> |
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
changeset
|
544 </xml> |
23 | 545 |
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:
13
diff
changeset
|
546 <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
parents:
13
diff
changeset
|
547 <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
parents:
13
diff
changeset
|
548 <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
parents:
13
diff
changeset
|
549 label="Restrict search of database to a given set of ID's" |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
550 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
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
551 <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)
peterjc
parents:
14
diff
changeset
|
552 <option value="gilist">GI identifiers</option> |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
553 <option value="negative_gilist">Negative GI identifiers</option> |
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
554 <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:
13
diff
changeset
|
555 </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:
13
diff
changeset
|
556 <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:
13
diff
changeset
|
557 <when value="gilist"> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
558 <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
parents:
13
diff
changeset
|
559 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:
13
diff
changeset
|
560 </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:
13
diff
changeset
|
561 <when value="negative_gilist"> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
562 <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:
13
diff
changeset
|
563 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:
13
diff
changeset
|
564 </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:
13
diff
changeset
|
565 <when value="seqidlist"> |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
566 <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:
13
diff
changeset
|
567 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:
13
diff
changeset
|
568 </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:
13
diff
changeset
|
569 </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:
13
diff
changeset
|
570 </xml> |
23 | 571 <!--Tokens--> |
572 <token name="@ADV_MATRIX_GAPCOSTS@"><![CDATA[ | |
573 #if str($adv_opts.matrix_gapcosts.matrix): | |
574 -matrix '${adv_opts.matrix_gapcosts.matrix}' | |
575 ${adv_opts.matrix_gapcosts.gap_costs} | |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
576 #end if |
23 | 577 ]]></token> |
578 | |
579 <token name="@ADV_QCOV_HSP_PERC@"><![CDATA[ | |
580 #if float(str($adv_opts.qcov_hsp_perc)) > 0: | |
581 -qcov_hsp_perc '${adv_opts.qcov_hsp_perc}' | |
582 #end if | |
583 ]]></token> | |
584 | |
585 <token name="@ADV_ID_LIST_FILTER@"><![CDATA[ | |
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:
13
diff
changeset
|
586 #if $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'negative_gilist': |
23 | 587 -negative_gilist '${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:
13
diff
changeset
|
588 #elif $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'gilist': |
23 | 589 -gilist '{$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:
13
diff
changeset
|
590 #elif $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'seqidlist': |
23 | 591 -seqidlist '${adv_opts.adv_optional_id_files_opts.seqidlist}' |
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:
13
diff
changeset
|
592 #end if |
23 | 593 ]]></token> |
594 | |
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
changeset
|
595 <token name="@THREADS@">-num_threads "\${GALAXY_SLOTS:-8}"</token> |
23 | 596 |
25 | 597 <token name="@QUERY@"><![CDATA[ |
598 #if $query.is_of_type('fasta.gz') and $query.ext != "fasta": | |
599 -query <(gunzip -c '${query}') | |
600 #else: | |
601 -query '${query}' | |
602 #end if | |
603 ]]></token> | |
604 | |
27
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
605 <!-- Implement -dbtype and -db command line options (in blastdbcmd) --> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
606 <token name="@DBCMD_OPTS@"><![CDATA[ |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
607 -dbtype "$db_opts.db_type" |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
608 #if $db_opts.db_origin.db_origin_selector=="db": |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
609 -db "${db_opts.db_origin.database.fields.path.replace(',',' ')}" |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
610 #else if $db_opts.db_origin.db_origin_selector=="histdb": |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
611 -db '${os.path.join($db_opts.db_origin.histdb.extra_files_path, "blastdb")}' |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
612 #end if |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
613 ]]></token> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
614 |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
615 <!-- Implement -db ... / -subject ... command line options --> |
23 | 616 <token name="@BLAST_DB_SUBJECT@"><![CDATA[ |
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
changeset
|
617 #if $db_opts.db_opts_selector == "db": |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
618 -db '${" ".join(str($db_opts.database.fields.path).split(","))}' |
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
changeset
|
619 #elif $db_opts.db_opts_selector == "histdb": |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
620 -db '${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.
peterjc
parents:
diff
changeset
|
621 #else: |
25 | 622 #if $db_opts.subject.is_of_type('fasta.gz') and $db_opts.subject.ext != "fasta": |
23 | 623 -subject <(gunzip -c '${$db_opts.subject}') |
624 #else: | |
625 -subject '${db_opts.subject}' | |
626 #end if | |
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
changeset
|
627 #end if |
23 | 628 ]]></token> |
629 | |
630 <token name="@BLAST_OUTPUT@"><![CDATA[ -out '$output1' | |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
changeset
|
631 ##Set the extended list here so when we add things, saved workflows are not affected |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
632 #if str($output.out_format)=="ext": |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
633 -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
parents:
11
diff
changeset
|
634 #elif str($output.out_format)=="cols" |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
635 ##Pick your own columns. Galaxy gives us it comma separated, BLAST+ wants space separated: |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
636 ##TODO - Can we catch the user picking no columns and raise an error here? |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
637 #set cols = (str($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
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
638 -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.
peterjc
parents:
diff
changeset
|
639 #else: |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
640 ## Note do not quote this as can be '0 -html' which is really two arguments |
23 | 641 -outfmt ${output.out_format} |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
changeset
|
642 #end if |
23 | 643 ]]></token> |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
644 <token name="@ADV_FILTER_QUERY@">$adv_opts.filter_query</token> |
23 | 645 <token name="@ADV_MAX_HITS@"><![CDATA[ |
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
changeset
|
646 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string |
25 | 647 ## |
648 ## Quoting BLAST 2.7.1+ output from "blastp --help" or "blastn --help": | |
649 ## | |
650 ## *** Formatting options | |
651 ## -num_descriptions <Integer, >=0> | |
652 ## Number of database sequences to show one-line descriptions for | |
653 ## Not applicable for outfmt > 4 | |
654 ## Default = `500' | |
655 ## * Incompatible with: max_target_seqs | |
656 ## -num_alignments <Integer, >=0> | |
657 ## Number of database sequences to show alignments for | |
658 ## Default = `250' | |
659 ## * Incompatible with: max_target_seqs | |
660 ## | |
661 ## *** Restrict search or results | |
662 ## | |
663 ## -max_target_seqs <Integer, >=1> | |
664 ## Maximum number of aligned sequences to keep | |
665 ## Not applicable for outfmt <= 4 | |
666 ## Default = `500' | |
667 ## * Incompatible with: num_descriptions, num_alignments | |
668 ## | |
669 ## So, taken at face value we do still need to treat the Text and HTML output | |
670 ## differently from the Tabular and XML, yet the treatment of these limits is | |
671 ## different (during search or after the search when writing the output): | |
672 ## https://blastedbio.blogspot.com/2015/12/blast-max-target-sequences-bug.html | |
673 ## | |
674 ## See also our user-facing help text. | |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
changeset
|
675 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
676 #if str($output.out_format) in ["6", "ext", "cols", "5"]: |
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
677 ## Most output formats use this, including tabular and XML: |
23 | 678 -max_target_seqs '${adv_opts.max_hits}' |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
679 #else |
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
680 ## Text and HTML output formats 0-4 currently need this instead: |
25 | 681 -num_descriptions '${adv_opts.max_hits}' -num_alignments '${adv_opts.max_hits}' |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
682 #end if |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
changeset
|
683 #end if |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
684 #if str($adv_opts.max_hsps) |
23 | 685 -max_hsps '${adv_opts.max_hsps}' |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
686 #end if |
23 | 687 ]]></token> |
688 <token name="@ADV_WORD_SIZE@"><![CDATA[ | |
689 #if str($adv_opts.word_size): | |
690 -word_size '${adv_opts.word_size}' | |
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
changeset
|
691 #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:
diff
changeset
|
692 $adv_opts.parse_deflines |
23 | 693 ]]></token> |
694 <token name="@ADV_WINDOW_SIZE@"><![CDATA[ | |
695 #if str($adv_opts.window_size): | |
696 -window_size '${adv_opts.window_size}' | |
697 #end if | |
698 ]]></token> | |
699 | |
700 <token name="@ADV_THRESHOLD@"><![CDATA[ | |
701 #if str($adv_opts.threshold): | |
702 -threshold '${adv_opts.threshold}' | |
703 #end if | |
704 ]]></token> | |
705 | |
706 <token name="@ADV_COMP_BASED_STATS@"><![CDATA[ | |
707 #if str($adv_opts.comp_based_stats): | |
708 -comp_based_stats '${adv_opts.comp_based_stats}' | |
709 #end if | |
710 ]]></token> | |
711 | |
712 <token name="@ADV_GAPOPEN@"><![CDATA[ | |
713 #if str($adv_opts.gapopen): | |
714 -gapopen '${adv_opts.gapopen}' | |
715 #end if | |
716 ]]></token> | |
717 | |
718 <token name="@ADV_GAPEXTEND@"><![CDATA[ | |
719 #if str($adv_opts.gapextend): | |
720 -gapextend '${adv_opts.gapextend}' | |
721 #end if | |
722 ]]></token> | |
723 | |
724 <token name="@ADV_MATRIX@"><![CDATA[ | |
725 #if str($adv_opts.matrix): | |
726 -matrix '${adv_opts.matrix}' | |
727 #end if | |
728 ]]></token> | |
729 | |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
changeset
|
730 <!-- @ON_DB_SUBJECT@ is for use with @BLAST_DB_SUBJECT@ --> |
23 | 731 <token name="@ON_DB_SUBJECT@"><![CDATA[ |
732 #if str($db_opts.db_opts_selector)=='db' | |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
733 '${db_opts.database}' |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
changeset
|
734 #elif str($db_opts.db_opts_selector)=='histdb' |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
735 '${db_opts.histdb.name}' |
11
4c4a0da938ff
Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25.
peterjc
parents:
diff
changeset
|
736 #else |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
737 '${db_opts.subject.name}' |
23 | 738 #end if |
739 ]]></token> | |
740 | |
27
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
741 <!-- @ON_DBCMD_OPTS@ is for use with @DBCMD_OPTS@ --> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
742 <token name="@ON_DBCMD_OPTS@"><![CDATA[ |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
743 #if str($db_opts.db_origin.db_origin_selector)=="db" |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
744 '${db_opts.db_origin.database}' |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
745 #else |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
746 '${db_opts.db_origin.histdb.name}' |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
747 #end if |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
748 ]]></token> |
6f8ea4b9a2c4
"planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 3f9f39ad808325a11d9967980d2cb82c96d69324"
peterjc
parents:
26
diff
changeset
|
749 |
23 | 750 <token name="@REFERENCES@"><![CDATA[ |
15
c16c30e9ad5b
Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc)
peterjc
parents:
14
diff
changeset
|
751 Peter J. A. Cock, John M. Chilton, Björn GrĂ¼ning, James E. Johnson, Nicola Soranzo (2015). |
17
697f40151eaf
v0.1.05 - Update citation information now GigaScience paper is out
peterjc
parents:
16
diff
changeset
|
752 NCBI BLAST+ integrated into Galaxy. *GigaScience* 4:39 |
23 | 753 https://doi.org/10.1186/s13742-015-0080-7 |
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
changeset
|
754 |
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
changeset
|
755 Christiam Camacho et al. (2009). |
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
changeset
|
756 BLAST+: architecture and applications. |
17
697f40151eaf
v0.1.05 - Update citation information now GigaScience paper is out
peterjc
parents:
16
diff
changeset
|
757 *BMC Bioinformatics* 15;10:421. |
23 | 758 https://doi.org/10.1186/1471-2105-10-421 |
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
changeset
|
759 |
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
changeset
|
760 This wrapper is available to install into other Galaxy Instances via the Galaxy |
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
changeset
|
761 Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus |
23 | 762 ]]></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:
13
diff
changeset
|
763 <xml name="blast_citations"> |
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
diff
changeset
|
764 <citations> |
23 | 765 <citation type="doi">10.1093/nar/25.17.3389</citation> |
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:
13
diff
changeset
|
766 <citation type="doi">10.1186/1471-2105-10-421</citation> |
17
697f40151eaf
v0.1.05 - Update citation information now GigaScience paper is out
peterjc
parents:
16
diff
changeset
|
767 <citation type="doi">10.1186/s13742-015-0080-7</citation> |
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:
13
diff
changeset
|
768 </citations> |
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
diff
changeset
|
769 </xml> |
23 | 770 <token name="@OUTPUT_FORMAT@"><![CDATA[ |
771 **Output 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.
peterjc
parents:
diff
changeset
|
772 |
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
changeset
|
773 Because Galaxy focuses on processing tabular data, the default output of this |
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
changeset
|
774 tool is tabular. The standard BLAST+ tabular output contains 12 columns: |
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
changeset
|
775 |
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
changeset
|
776 ====== ========= ============================================ |
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
changeset
|
777 Column NCBI name Description |
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
changeset
|
778 ------ --------- -------------------------------------------- |
23 | 779 1 qaccver Query accession dot version |
780 2 saccver Subject accession dot version (database hit) | |
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
changeset
|
781 3 pident Percentage of identical matches |
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
changeset
|
782 4 length Alignment length |
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
changeset
|
783 5 mismatch Number of mismatches |
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
changeset
|
784 6 gapopen Number of gap openings |
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
changeset
|
785 7 qstart Start of alignment in query |
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
changeset
|
786 8 qend End of alignment in query |
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
changeset
|
787 9 sstart Start of alignment in subject (database hit) |
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
changeset
|
788 10 send End of alignment in subject (database hit) |
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
changeset
|
789 11 evalue Expectation value (E-value) |
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
changeset
|
790 12 bitscore Bit score |
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
changeset
|
791 ====== ========= ============================================ |
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
changeset
|
792 |
23 | 793 Until BLAST+ 2.5.0, the first two columns were ``qseqid`` and ``sseqid``, |
794 which were usually strings contained multiple pipe-separated entries. | |
795 In BLAST+ 2.5.0, the first two columns became ``qacc`` and ``sacc`` | |
796 (accesion only), while in BLAST+ 2.6.0 this was changed again to use | |
797 ``qaccver`` and ``saccver`` (accession dot version). | |
798 | |
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
changeset
|
799 The BLAST+ tools can optionally output additional columns of information, |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
800 but this takes longer to calculate. Many commonly used extra columns are |
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
changeset
|
801 included by selecting the extended tabular output. The extra columns are |
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
changeset
|
802 included *after* the standard 12 columns. This is so that you can write |
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
changeset
|
803 workflow filtering steps that accept either the 12 or 25 column tabular |
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
changeset
|
804 BLAST output. Galaxy now uses this extended 25 column output by default. |
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
changeset
|
805 |
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
changeset
|
806 ====== ============= =========================================== |
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
changeset
|
807 Column NCBI name Description |
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
changeset
|
808 ------ ------------- ------------------------------------------- |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
809 13 sallseqid All subject Seq-id(s), separated by a ';' |
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
changeset
|
810 14 score Raw score |
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
changeset
|
811 15 nident Number of identical matches |
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
changeset
|
812 16 positive Number of positive-scoring matches |
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
changeset
|
813 17 gaps Total number of gaps |
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
changeset
|
814 18 ppos Percentage of positive-scoring matches |
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
changeset
|
815 19 qframe Query frame |
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
changeset
|
816 20 sframe Subject frame |
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
changeset
|
817 21 qseq Aligned part of query sequence |
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
changeset
|
818 22 sseq Aligned part of subject sequence |
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
changeset
|
819 23 qlen Query sequence length |
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
changeset
|
820 24 slen Subject sequence length |
23 | 821 25 salltitles All subject title(s), separated by a '<>' |
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
changeset
|
822 ====== ============= =========================================== |
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
changeset
|
823 |
13
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
824 The third option is to customise the tabular output by selecting which |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
825 columns you want, from the standard set of 12, the default set of 25, |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
826 or any of the additional columns BLAST+ offers (including species name). |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
827 |
623f727cdff1
Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields.
peterjc
parents:
11
diff
changeset
|
828 The fourth option is BLAST XML output, which is designed to be parsed by |
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
changeset
|
829 another program, and is understood by some Galaxy tools. |
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
changeset
|
830 |
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
changeset
|
831 You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program). |
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
changeset
|
832 The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website. |
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
changeset
|
833 The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query. |
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
changeset
|
834 The two query anchored outputs show a multiple sequence alignment between the query and all the matches, |
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
changeset
|
835 and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences). |
23 | 836 ]]></token> |
837 <token name="@FASTA_WARNING@"><![CDATA[ | |
838 .. class:: warningmark | |
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
changeset
|
839 |
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
changeset
|
840 You can also search against a FASTA file of subject (target) |
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
changeset
|
841 sequences. This is *not* advised because it is slower (only one |
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
changeset
|
842 CPU is used), but more importantly gives e-values for pairwise |
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
changeset
|
843 searches (very small e-values which will look overly signficiant). |
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
changeset
|
844 In most cases you should instead turn the other FASTA file into a |
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
changeset
|
845 database first using *makeblastdb* and search against that. |
23 | 846 ]]></token> |
847 <token name="@SEARCH_TIME_WARNING@"><![CDATA[ | |
848 .. class:: warningmark | |
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
changeset
|
849 |
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
changeset
|
850 **Note**. Database searches may take a substantial amount of time. |
22
6f386c5dc4fb
v0.2.01 add -max_hsps, -use_sw_tback; lists args; internal updates
peterjc
parents:
21
diff
changeset
|
851 For large input datasets it is advisable to allow overnight processing. |
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
changeset
|
852 |
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
changeset
|
853 ----- |
23 | 854 ]]></token> |
855 <token name="@CLI_OPTIONS@"><![CDATA[ | |
856 **Advanced Options** | |
857 | |
858 For help with advanced options and their default values, visit the | |
859 NCBI BLAST® Command Line Applications User Manual, Appendices, | |
860 `Options for the command-line applications | |
861 <https://www.ncbi.nlm.nih.gov/books/NBK279684/#_appendices_Options_for_the_commandline_a_>`_. | |
862 | |
863 For amino acid substitution matrices, see `BLAST Substitution Matrices | |
864 <https://www.ncbi.nlm.nih.gov/books/NBK279684/#_appendices_BLAST_Substitution_Matrices_>`_ in the same | |
865 appendices. | |
866 | |
867 ]]></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.
peterjc
parents:
diff
changeset
|
868 </macros> |