Mercurial > repos > devteam > ncbi_blast_plus

annotate tools/ncbi_blast_plus/ncbi_macros.xml @ 17:fc571deae017 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 9e989fb08bbd04732d94688d00e781d58949508f-dirty
author peterjc
date Mon, 03 Apr 2017 15:31:27 -0400
parents 4dcc9429d6d2
children c5f20ca77de2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
1 <macros>
13
4dcc9429d6d2 v0.2.00, updated to depend on BLAST+ 2.5.0
peterjc
parents: 12
diff changeset
2 <token name="@WRAPPER_VERSION@">0.2.00</token>
6
856b73016ba1 v0.1.05 - Update citation information now GigaScience paper is out
peterjc
parents: 5
diff changeset
3 <xml name="parallelism">
856b73016ba1 v0.1.05 - Update citation information now GigaScience paper is out
peterjc
parents: 5
diff changeset
4 <!-- If job splitting is enabled, break up the query file into parts -->
856b73016ba1 v0.1.05 - Update citation information now GigaScience paper is out
peterjc
parents: 5
diff changeset
5 <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1" />
856b73016ba1 v0.1.05 - Update citation information now GigaScience paper is out
peterjc
parents: 5
diff changeset
6 </xml>
3
e98f6bd363ba planemo upload for repository https://github.com/peterjc/galaxy_blast/tools/ncbi_blast_plus commit a567843bb239ee8faec72eb7e52f3b5aa3191631
peterjc
parents: 2
diff changeset
7 <xml name="preamble">
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
8 <requirements>
13
4dcc9429d6d2 v0.2.00, updated to depend on BLAST+ 2.5.0
peterjc
parents: 12
diff changeset
9 <requirement type="package" version="2.5.0">blast</requirement>
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
10 </requirements>
3
e98f6bd363ba planemo upload for repository https://github.com/peterjc/galaxy_blast/tools/ncbi_blast_plus commit a567843bb239ee8faec72eb7e52f3b5aa3191631
peterjc
parents: 2
diff changeset
11 <stdio>
e98f6bd363ba planemo upload for repository https://github.com/peterjc/galaxy_blast/tools/ncbi_blast_plus commit a567843bb239ee8faec72eb7e52f3b5aa3191631
peterjc
parents: 2
diff changeset
12 <!-- Anything other than zero is an error -->
e98f6bd363ba planemo upload for repository https://github.com/peterjc/galaxy_blast/tools/ncbi_blast_plus commit a567843bb239ee8faec72eb7e52f3b5aa3191631
peterjc
parents: 2
diff changeset
13 <exit_code range="1:" />
e98f6bd363ba planemo upload for repository https://github.com/peterjc/galaxy_blast/tools/ncbi_blast_plus commit a567843bb239ee8faec72eb7e52f3b5aa3191631
peterjc
parents: 2
diff changeset
14 <!-- Might see negative return codes for Unix signals via Python subprocess -->
e98f6bd363ba planemo upload for repository https://github.com/peterjc/galaxy_blast/tools/ncbi_blast_plus commit a567843bb239ee8faec72eb7e52f3b5aa3191631
peterjc
parents: 2
diff changeset
15 <exit_code range=":-1" />
e98f6bd363ba planemo upload for repository https://github.com/peterjc/galaxy_blast/tools/ncbi_blast_plus commit a567843bb239ee8faec72eb7e52f3b5aa3191631
peterjc
parents: 2
diff changeset
16 <!-- In case the return code has not been set properly check stderr too -->
e98f6bd363ba planemo upload for repository https://github.com/peterjc/galaxy_blast/tools/ncbi_blast_plus commit a567843bb239ee8faec72eb7e52f3b5aa3191631
peterjc
parents: 2
diff changeset
17 <regex match="Error:" />
e98f6bd363ba planemo upload for repository https://github.com/peterjc/galaxy_blast/tools/ncbi_blast_plus commit a567843bb239ee8faec72eb7e52f3b5aa3191631
peterjc
parents: 2
diff changeset
18 <regex match="Exception:" />
e98f6bd363ba planemo upload for repository https://github.com/peterjc/galaxy_blast/tools/ncbi_blast_plus commit a567843bb239ee8faec72eb7e52f3b5aa3191631
peterjc
parents: 2
diff changeset
19 </stdio>
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
20 <version_command>@BINARY@ -version</version_command>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
21 </xml>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
22 <xml name="output_change_format">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
23 <change_format>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
24 <when input="output.out_format" value="0" format="txt"/>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
25 <when input="output.out_format" value="0 -html" format="html"/>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
26 <when input="output.out_format" value="2" format="txt"/>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
27 <when input="output.out_format" value="2 -html" format="html"/>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
28 <when input="output.out_format" value="4" format="txt"/>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
29 <when input="output.out_format" value="4 -html" format="html"/>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
30 <when input="output.out_format" value="5" format="blastxml"/>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
31 </change_format>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
32 </xml>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
33 <xml name="input_out_format">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
34 <conditional name="output">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
35 <param name="out_format" type="select" label="Output format">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
36 <option value="6">Tabular (standard 12 columns)</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
37 <option value="ext" selected="True">Tabular (extended 25 columns)</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
38 <option value="cols">Tabular (select which columns)</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
39 <option value="5">BLAST XML</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
40 <option value="0">Pairwise text</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
41 <option value="0 -html">Pairwise HTML</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
42 <option value="2">Query-anchored text</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
43 <option value="2 -html">Query-anchored HTML</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
44 <option value="4">Flat query-anchored text</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
45 <option value="4 -html">Flat query-anchored HTML</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
46 <!--
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
47 <option value="-outfmt 11">BLAST archive format (ASN.1)</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
48 -->
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
49 </param>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
50 <when value="6"/>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
51 <when value="ext"/>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
52 <when value="cols">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
53 <param name="std_cols" type="select" multiple="true" display="checkboxes" label="Standard columns">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
54 <option selected="true" value="qseqid">qseqid = Query Seq-id (ID of your sequence)</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
55 <option selected="true" value="sseqid">sseqid = Subject Seq-id (ID of the database hit)</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
56 <option selected="true" value="pident">pident = Percentage of identical matches</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
57 <option selected="true" value="length">length = Alignment length</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
58 <option selected="true" value="mismatch">mismatch = Number of mismatches</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
59 <option selected="true" value="gapopen">gapopen = Number of gap openings</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
60 <option selected="true" value="qstart">qstart = Start of alignment in query</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
61 <option selected="true" value="qend">qend = End of alignment in query</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
62 <option selected="true" value="sstart">sstart = Start of alignment in subject (database hit)</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
63 <option selected="true" value="send">send = End of alignment in subject (database hit)</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
64 <option selected="true" value="evalue">evalue = Expectation value (E-value)</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
65 <option selected="true" value="bitscore">bitscore = Bit score</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
66 </param>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
67 <param name="ext_cols" type="select" multiple="true" display="checkboxes" label="Extended columns">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
68 <option value="sallseqid">sallseqid = All subject Seq-id(s), separated by a ';'</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
69 <option value="score">score = Raw score</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
70 <option value="nident">nident = Number of identical matches</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
71 <option value="positive">positive = Number of positive-scoring matches</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
72 <option value="gaps">gaps = Total number of gaps</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
73 <option value="ppos">ppos = Percentage of positive-scoring matches</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
74 <option value="qframe">qframe = Query frame</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
75 <option value="sframe">sframe = Subject frame</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
76 <option value="qseq">qseq = Aligned part of query sequence</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
77 <option value="sseq">sseq = Aligned part of subject sequence</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
78 <option value="qlen">qlen = Query sequence length</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
79 <option value="slen">slen = Subject sequence length</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
80 <option value="salltitles">salltitles = All subject title(s), separated by a '&lt;&gt;'</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
81 </param>
2
6119ddccd8a3 Uploaded v0.1.02 preview 3, disable tests using blastdb*.loc since not supported on the ToolShed (yet).
peterjc
parents: 0
diff changeset
82 <param name="ids_cols" type="select" multiple="true" display="checkboxes" label="Other identifier columns">
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
83 <option value="qgi">qgi = Query GI</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
84 <option value="qacc">qacc = Query accesion</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
85 <option value="qaccver">qaccver = Query accesion.version</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
86 <option value="sallseqid">sallseqid = All subject Seq-id(s), separated by a ';'</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
87 <option value="sgi">sgi = Subject GI</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
88 <option value="sallgi">sallgi = All subject GIs</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
89 <option value="sacc">sacc = Subject accession</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
90 <option value="saccver">saccver = Subject accession.version</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
91 <option value="sallacc">sallacc = All subject accessions</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
92 <option value="stitle">stitle = Subject Title</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
93 </param>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
94 <param name="misc_cols" type="select" multiple="true" display="checkboxes" label="Miscellaneous columns">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
95 <option value="sstrand">sstrand = Subject Strand</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
96 <!-- Is it really worth including 'frames' given have 'qframe' and 'sframe'? -->
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
97 <option value="frames">frames = Query and subject frames separated by a '/'</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
98 <option value="btop">btop = Blast traceback operations (BTOP)</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
99 <option value="qcovs">qcovs = Query Coverage Per Subject</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
100 <option value="qcovhsp">qcovhsp = Query Coverage Per HSP</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
101 </param>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
102 <param name="tax_cols" type="select" multiple="true" display="checkboxes" label="Taxonomy columns">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
103 <option value="staxids">staxids = unique Subject Taxonomy ID(s), separated by a ';' (in numerical order)</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
104 <!-- TODO, how to handle the taxonomy data file dependency? If missing these give N/A -->
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
105 <option value="sscinames">sscinames = unique Subject Scientific Name(s), separated by a ';'</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
106 <option value="scomnames">scomnames = unique Subject Common Name(s), separated by a ';'</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
107 <option value="sblastnames">sblastnames = unique Subject Blast Name(s), separated by a ';' (in alphabetical order)</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
108 <option value="sskingdoms">sskingdoms = unique Subject Super Kingdom(s), separated by a ';' (in alphabetical order)</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
109 </param>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
110 </when>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
111 <when value="5"/>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
112 <when value="0"/>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
113 <when value="0 -html"/>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
114 <when value="2"/>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
115 <when value="2 -html"/>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
116 <when value="4"/>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
117 <when value="4 -html"/>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
118 </conditional>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
119 </xml>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
120 <xml name="input_scoring_matrix">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
121 <param name="matrix" type="select" label="Scoring matrix">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
122 <option value="BLOSUM90">BLOSUM90</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
123 <option value="BLOSUM80">BLOSUM80</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
124 <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
125 <option value="BLOSUM50">BLOSUM50</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
126 <option value="BLOSUM45">BLOSUM45</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
127 <option value="PAM250">PAM250</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
128 <option value="PAM70">PAM70</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
129 <option value="PAM30">PAM30</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
130 </param>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
131 </xml>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
132 <xml name="input_query_gencode">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
133 <param name="query_gencode" type="select" label="Query genetic code">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
134 <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->
12
d8f2c1f560ec Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents: 10
diff changeset
135 <option value="1" selected="True">1. Standard</option>
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
136 <option value="2">2. Vertebrate Mitochondrial</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
137 <option value="3">3. Yeast Mitochondrial</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
138 <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
139 <option value="5">5. Invertebrate Mitochondrial</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
140 <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
141 <option value="9">9. Echinoderm Mitochondrial</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
142 <option value="10">10. Euplotid Nuclear</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
143 <option value="11">11. Bacteria and Archaea</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
144 <option value="12">12. Alternative Yeast Nuclear</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
145 <option value="13">13. Ascidian Mitochondrial</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
146 <option value="14">14. Flatworm Mitochondrial</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
147 <option value="15">15. Blepharisma Macronuclear</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
148 <option value="16">16. Chlorophycean Mitochondrial Code</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
149 <option value="21">21. Trematode Mitochondrial Code</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
150 <option value="22">22. Scenedesmus obliquus mitochondrial Code</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
151 <option value="23">23. Thraustochytrium Mitochondrial Code</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
152 <option value="24">24. Pterobranchia mitochondrial code</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
153 </param>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
154 </xml>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
155 <xml name="input_db_gencode">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
156 <param name="db_gencode" type="select" label="Database/subject genetic code">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
157 <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->
12
d8f2c1f560ec Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents: 10
diff changeset
158 <option value="1" selected="True">1. Standard</option>
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
159 <option value="2">2. Vertebrate Mitochondrial</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
160 <option value="3">3. Yeast Mitochondrial</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
161 <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
162 <option value="5">5. Invertebrate Mitochondrial</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
163 <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
164 <option value="9">9. Echinoderm Mitochondrial</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
165 <option value="10">10. Euplotid Nuclear</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
166 <option value="11">11. Bacteria and Archaea</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
167 <option value="12">12. Alternative Yeast Nuclear</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
168 <option value="13">13. Ascidian Mitochondrial</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
169 <option value="14">14. Flatworm Mitochondrial</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
170 <option value="15">15. Blepharisma Macronuclear</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
171 <option value="16">16. Chlorophycean Mitochondrial Code</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
172 <option value="21">21. Trematode Mitochondrial Code</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
173 <option value="22">22. Scenedesmus obliquus mitochondrial Code</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
174 <option value="23">23. Thraustochytrium Mitochondrial Code</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
175 <option value="24">24. Pterobranchia mitochondrial code</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
176 </param>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
177 </xml>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
178 <xml name="input_conditional_nucleotide_db">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
179 <conditional name="db_opts">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
180 <param name="db_opts_selector" type="select" label="Subject database/sequences">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
181 <option value="db" selected="True">Locally installed BLAST database</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
182 <option value="histdb">BLAST database from your history</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
183 <option value="file">FASTA file from your history (see warning note below)</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
184 </param>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
185 <when value="db">
10
e6337ef07e9a v0.1.08 can search against multiple locally installed databases
peterjc
parents: 9
diff changeset
186 <param name="database" type="select" multiple="true" label="Nucleotide BLAST database">
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
187 <options from_data_table="blastdb" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
188 </param>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
189 <param name="histdb" type="hidden" value="" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
190 <param name="subject" type="hidden" value="" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
191 </when>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
192 <when value="histdb">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
193 <param name="database" type="hidden" value="" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
194 <param name="histdb" type="data" format="blastdbn" label="Nucleotide BLAST database" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
195 <param name="subject" type="hidden" value="" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
196 </when>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
197 <when value="file">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
198 <param name="database" type="hidden" value="" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
199 <param name="histdb" type="hidden" value="" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
200 <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
201 </when>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
202 </conditional>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
203 </xml>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
204 <xml name="input_conditional_protein_db">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
205 <conditional name="db_opts">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
206 <param name="db_opts_selector" type="select" label="Subject database/sequences">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
207 <option value="db" selected="True">Locally installed BLAST database</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
208 <option value="histdb">BLAST database from your history</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
209 <option value="file">FASTA file from your history (see warning note below)</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
210 </param>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
211 <when value="db">
10
e6337ef07e9a v0.1.08 can search against multiple locally installed databases
peterjc
parents: 9
diff changeset
212 <param name="database" type="select" multiple="true" label="Protein BLAST database">
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
213 <options from_data_table="blastdb_p" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
214 </param>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
215 <param name="histdb" type="hidden" value="" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
216 <param name="subject" type="hidden" value="" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
217 </when>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
218 <when value="histdb">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
219 <param name="database" type="hidden" value="" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
220 <param name="histdb" type="data" format="blastdbp" label="Protein BLAST database" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
221 <param name="subject" type="hidden" value="" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
222 </when>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
223 <when value="file">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
224 <param name="database" type="hidden" value="" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
225 <param name="histdb" type="hidden" value="" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
226 <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
227 </when>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
228 </conditional>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
229 </xml>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
230 <xml name="input_conditional_pssm">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
231 <conditional name="db_opts">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
232 <param name="db_opts_selector" type="select" label="Protein domain database (PSSM)">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
233 <option value="db" selected="True">Locally installed BLAST protein domain database</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
234 <option value="histdb">BLAST protein domain database from your history</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
235 </param>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
236 <when value="db">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
237 <param name="database" type="select" label="Protein domain database">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
238 <options from_data_table="blastdb_d" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
239 </param>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
240 <param name="histdb" type="hidden" value="" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
241 <param name="subject" type="hidden" value="" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
242 </when>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
243 <when value="histdb">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
244 <param name="database" type="hidden" value="" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
245 <param name="histdb" type="data" format="blastdbd" label="Protein domain database" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
246 <param name="subject" type="hidden" value="" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
247 </when>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
248 </conditional>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
249 </xml>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
250 <xml name="input_conditional_choose_db_type">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
251 <conditional name="db_opts">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
252 <param name="db_type" type="select" label="Type of BLAST database">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
253 <option value="nucl" selected="True">Nucleotide</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
254 <option value="prot">Protein</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
255 </param>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
256 <when value="nucl">
10
e6337ef07e9a v0.1.08 can search against multiple locally installed databases
peterjc
parents: 9
diff changeset
257 <param name="database" type="select" multiple="true" label="Nucleotide BLAST database">
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
258 <options from_data_table="blastdb" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
259 </param>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
260 </when>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
261 <when value="prot">
10
e6337ef07e9a v0.1.08 can search against multiple locally installed databases
peterjc
parents: 9
diff changeset
262 <param name="database" type="select" multiple="true" label="Protein BLAST database">
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
263 <options from_data_table="blastdb_p" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
264 </param>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
265 </when>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
266 </conditional>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
267 </xml>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
268 <xml name="input_parse_deflines">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
269 <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
270 </xml>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
271 <xml name="input_filter_query_default_false">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
272 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
273 </xml>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
274 <xml name="input_filter_query_default_true">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
275 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
276 </xml>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
277 <xml name="input_max_hits">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
278 <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
279 <validator type="in_range" min="0" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
280 </param>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
281 </xml>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
282 <xml name="input_evalue">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
283 <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
284 </xml>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
285 <xml name="input_word_size">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
286 <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2.">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
287 <validator type="in_range" min="0" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
288 </param>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
289 </xml>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
290 <xml name="input_strand">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
291 <param name="strand" type="select" label="Query strand(s) to search against database/subject">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
292 <option value="-strand both">Both</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
293 <option value="-strand plus">Plus (forward)</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
294 <option value="-strand minus">Minus (reverse complement)</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
295 </param>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
296 </xml>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
297 <xml name="input_qcov_hsp_perc">
12
d8f2c1f560ec Uploaded v0.1.08, can search multiple local databases, fixes a pipe problem in blastdbcmd, and minor internal changes.
peterjc
parents: 10
diff changeset
298 <param name="qcov_hsp_perc" type="float" value="0" min="0" max="100" label="Minimum query coverage per hsp (percentage, 0 to 100)" help="See also the output column qcovhsp"/>
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
299 </xml>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
300 <xml name="advanced_options">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
301 <conditional name="adv_opts">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
302 <param name="adv_opts_selector" type="select" label="Advanced Options">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
303 <option value="basic" selected="True">Hide Advanced Options</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
304 <option value="advanced">Show Advanced Options</option>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
305 </param>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
306 <when value="basic" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
307 <when value="advanced">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
308 <yield />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
309 </when>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
310 </conditional>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
311 </xml>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
312 <xml name="advanced_optional_id_files">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
313 <conditional name="adv_optional_id_files_opts">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
314 <param name="adv_optional_id_files_opts_selector" type="select"
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
315 label="Restrict search of database to a given set of ID's"
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
316 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.">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
317 <option value="none" selected="True">No restriction, search the entire database</option>
2
6119ddccd8a3 Uploaded v0.1.02 preview 3, disable tests using blastdb*.loc since not supported on the ToolShed (yet).
peterjc
parents: 0
diff changeset
318 <option value="gilist">GI identifiers</option>
6119ddccd8a3 Uploaded v0.1.02 preview 3, disable tests using blastdb*.loc since not supported on the ToolShed (yet).
peterjc
parents: 0
diff changeset
319 <option value="negative_gilist">Negative GI identifiers</option>
6119ddccd8a3 Uploaded v0.1.02 preview 3, disable tests using blastdb*.loc since not supported on the ToolShed (yet).
peterjc
parents: 0
diff changeset
320 <option value="seqidlist">Sequence identifiers (SeqId's)</option>
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
321 </param>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
322 <when value="none" />
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
323 <when value="gilist">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
324 <param name="gilist" type="data" format="txt" label="Restrict search of database to GI's listed in this file"
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
325 help="This option is only available for database searches."/>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
326 </when>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
327 <when value="negative_gilist">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
328 <param name="negative_gilist" type="data" format="txt" label="Restrict search of database to everything except the GI's listed in this file"
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
329 help="This option is only available for database searches."/>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
330 </when>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
331 <when value="seqidlist">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
332 <param name="seqidlist" type="data" format="txt" label=" Restrict search of database to list of SeqId's"
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
333 help="This option is only available for database searches."/>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
334 </when>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
335 </conditional>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
336 </xml>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
337 <token name="@ADV_QCOV_HSP_PERC@">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
338 #if float(str($adv_opts.qcov_hsp_perc)) &gt; 0:
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
339 -qcov_hsp_perc $adv_opts.qcov_hsp_perc
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
340 #end if
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
341 </token>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
342 <token name="@ADV_ID_LIST_FILTER@">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
343 #if $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'negative_gilist':
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
344 -negative_gilist $adv_opts.adv_optional_id_files_opts.negative_gilist
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
345 #elif $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'gilist':
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
346 -gilist $adv_opts.adv_optional_id_files_opts.gilist
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
347 #elif $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'seqidlist':
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
348 -seqidlist $adv_opts.adv_optional_id_files_opts.seqidlist
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
349 #end if
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
350 </token>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
351 <token name="@THREADS@">-num_threads "\${GALAXY_SLOTS:-8}"</token>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
352 <token name="@BLAST_DB_SUBJECT@">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
353 #if $db_opts.db_opts_selector == "db":
10
e6337ef07e9a v0.1.08 can search against multiple locally installed databases
peterjc
parents: 9
diff changeset
354 -db "${' '.join(str( $db_opts.database.fields.path ).split( ',' ))}"
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
355 #elif $db_opts.db_opts_selector == "histdb":
5
188d2aca045b Uploaded v0.1.04, fix regression with BLAST database from history
peterjc
parents: 3
diff changeset
356 -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}"
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
357 #else:
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
358 -subject "$db_opts.subject"
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
359 #end if
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
360 </token>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
361 <token name="@BLAST_OUTPUT@">-out "$output1"
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
362 ##Set the extended list here so when we add things, saved workflows are not affected
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
363 #if str($output.out_format)=="ext":
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
364 -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen salltitles"
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
365 #elif str($output.out_format)=="cols"
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
366 ##Pick your own columns. Galaxy gives us it comma separated, BLAST+ wants space separated:
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
367 ##TODO - Can we catch the user picking no columns and raise an error here?
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
368 #set cols = (str($output.std_cols)+","+str($output.ext_cols)+","+str($output.ids_cols)+","+str($output.misc_cols)+","+str($output.tax_cols)).replace("None", "").replace(",,", ",").replace(",", " ").strip()
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
369 -outfmt "6 $cols"
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
370 #else:
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
371 -outfmt $output.out_format
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
372 #end if
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
373 </token>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
374 <token name="@ADV_FILTER_QUERY@">$adv_opts.filter_query</token>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
375 <token name="@ADV_MAX_HITS@">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
376 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
377 ## Note -max_target_seqs used to simply override -num_descriptions and -num_alignments
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
378 ## but this was changed in BLAST+ 2.2.27 onwards to force their use (raised with NCBI)
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
379 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
380 #if str($output.out_format) in ["6", "ext", "cols", "5"]:
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
381 ## Most output formats use this, including tabular and XML:
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
382 -max_target_seqs $adv_opts.max_hits
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
383 #else
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
384 ## Text and HTML output formats 0-4 currently need this instead:
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
385 -num_descriptions $adv_opts.max_hits -num_alignments $adv_opts.max_hits
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
386 #end if
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
387 #end if
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
388 </token>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
389 <token name="@ADV_WORD_SIZE@">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
390 #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
391 -word_size $adv_opts.word_size
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
392 #end if
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
393 $adv_opts.parse_deflines
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
394 </token>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
395 <!-- @ON_DB_SUBJECT@ is for use with @BLAST_DB_SUBJECT@ -->
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
396 <token name="@ON_DB_SUBJECT@">#if str($db_opts.db_opts_selector)=='db'
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
397 ${db_opts.database}
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
398 #elif str($db_opts.db_opts_selector)=='histdb'
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
399 ${db_opts.histdb.name}
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
400 #else
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
401 ${db_opts.subject.name}
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
402 #end if</token>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
403 <token name="@REFERENCES@">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
404 Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo (2015).
6
856b73016ba1 v0.1.05 - Update citation information now GigaScience paper is out
peterjc
parents: 5
diff changeset
405 NCBI BLAST+ integrated into Galaxy. *GigaScience* 4:39
856b73016ba1 v0.1.05 - Update citation information now GigaScience paper is out
peterjc
parents: 5
diff changeset
406 http://dx.doi.org/10.1186/s13742-015-0080-7
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
407
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
408 Christiam Camacho et al. (2009).
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
409 BLAST+: architecture and applications.
6
856b73016ba1 v0.1.05 - Update citation information now GigaScience paper is out
peterjc
parents: 5
diff changeset
410 *BMC Bioinformatics* 15;10:421.
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
411 http://dx.doi.org/10.1186/1471-2105-10-421
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
412
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
413 This wrapper is available to install into other Galaxy Instances via the Galaxy
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
414 Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
415 </token>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
416 <xml name="blast_citations">
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
417 <citations>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
418 <citation type="doi">10.1186/1471-2105-10-421</citation>
6
856b73016ba1 v0.1.05 - Update citation information now GigaScience paper is out
peterjc
parents: 5
diff changeset
419 <citation type="doi">10.1186/s13742-015-0080-7</citation>
0
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
420 </citations>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
421 </xml>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
422 <token name="@OUTPUT_FORMAT@">**Output format**
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
423
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
424 Because Galaxy focuses on processing tabular data, the default output of this
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
425 tool is tabular. The standard BLAST+ tabular output contains 12 columns:
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
426
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
427 ====== ========= ============================================
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
428 Column NCBI name Description
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
429 ------ --------- --------------------------------------------
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
430 1 qseqid Query Seq-id (ID of your sequence)
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
431 2 sseqid Subject Seq-id (ID of the database hit)
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
432 3 pident Percentage of identical matches
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
433 4 length Alignment length
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
434 5 mismatch Number of mismatches
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
435 6 gapopen Number of gap openings
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
436 7 qstart Start of alignment in query
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
437 8 qend End of alignment in query
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
438 9 sstart Start of alignment in subject (database hit)
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
439 10 send End of alignment in subject (database hit)
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
440 11 evalue Expectation value (E-value)
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
441 12 bitscore Bit score
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
442 ====== ========= ============================================
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
443
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
444 The BLAST+ tools can optionally output additional columns of information,
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
445 but this takes longer to calculate. Many commonly used extra columns are
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
446 included by selecting the extended tabular output. The extra columns are
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
447 included *after* the standard 12 columns. This is so that you can write
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
448 workflow filtering steps that accept either the 12 or 25 column tabular
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
449 BLAST output. Galaxy now uses this extended 25 column output by default.
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
450
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
451 ====== ============= ===========================================
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
452 Column NCBI name Description
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
453 ------ ------------- -------------------------------------------
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
454 13 sallseqid All subject Seq-id(s), separated by a ';'
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
455 14 score Raw score
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
456 15 nident Number of identical matches
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
457 16 positive Number of positive-scoring matches
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
458 17 gaps Total number of gaps
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
459 18 ppos Percentage of positive-scoring matches
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
460 19 qframe Query frame
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
461 20 sframe Subject frame
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
462 21 qseq Aligned part of query sequence
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
463 22 sseq Aligned part of subject sequence
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
464 23 qlen Query sequence length
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
465 24 slen Subject sequence length
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
466 25 salltitles All subject title(s), separated by a '&lt;&gt;'
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
467 ====== ============= ===========================================
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
468
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
469 The third option is to customise the tabular output by selecting which
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
470 columns you want, from the standard set of 12, the default set of 25,
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
471 or any of the additional columns BLAST+ offers (including species name).
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
472
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
473 The fourth option is BLAST XML output, which is designed to be parsed by
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
474 another program, and is understood by some Galaxy tools.
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
475
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
476 You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
477 The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
478 The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
479 The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
480 and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
481 </token>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
482 <token name="@FASTA_WARNING@">.. class:: warningmark
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
483
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
484 You can also search against a FASTA file of subject (target)
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
485 sequences. This is *not* advised because it is slower (only one
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
486 CPU is used), but more importantly gives e-values for pairwise
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
487 searches (very small e-values which will look overly signficiant).
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
488 In most cases you should instead turn the other FASTA file into a
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
489 database first using *makeblastdb* and search against that.
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
490 </token>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
491 <token name="@SEARCH_TIME_WARNING@">.. class:: warningmark
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
492
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
493 **Note**. Database searches may take a substantial amount of time.
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
494 For large input datasets it is advisable to allow overnight processing.
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
495
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
496 -----
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
497 </token>
432ea9614cc9 Uploaded v0.1.02 preview 1, using tool_data_table_conf.xml for loc files, etc
peterjc
parents:
diff changeset
498 </macros>