ncbi_blast_plus: tools/ncbi_blast_plus/ncbi

annotate tools/ncbi_blast_plus/ncbi_macros.xml @ 19:7f3c448e119b draft

v0.1.07 - fix macro problem in blastxml_to_tabular.xml, reenable .loc tests

author	peterjc
date	Thu, 19 Nov 2015 06:30:35 -0500
parents	577d9c12411a
children	3034ce97dd33

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>
19 7f3c448e119b v0.1.07 - fix macro problem in blastxml_to_tabular.xml, reenable .loc tests peterjc parents: 18 diff changeset	2 <token name="@WRAPPER_VERSION@">0.1.07</token>
17 697f40151eaf v0.1.05 - Update citation information now GigaScience paper is out peterjc parents: 16 diff changeset	3 <xml name="parallelism">
697f40151eaf v0.1.05 - Update citation information now GigaScience paper is out peterjc parents: 16 diff changeset	4 <!-- 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	5 <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	6 </xml>
15 c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	7 <xml name="preamble">
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	8 <requirements>
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	9 <requirement type="binary">@BINARY@</requirement>
18 577d9c12411a v0.1.06, now using BLAST+ 2.2.31 peterjc parents: 17 diff changeset	10 <requirement type="package" version="2.2.31">blast+</requirement>
15 c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	11 </requirements>
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	12 <stdio>
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	13 <!-- Anything other than zero is an error -->
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	14 <exit_code range="1:" />
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	15 <!-- Might see negative return codes for Unix signals via Python subprocess -->
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	16 <exit_code range=":-1" />
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	17 <!-- In case the return code has not been set properly check stderr too -->
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	18 <regex match="Error:" />
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	19 <regex match="Exception:" />
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	20 </stdio>
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	21 <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	22 </xml>
11 4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	23 <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	24 <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	25 <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	26 <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	27 <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	28 <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	29 <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	30 <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	31 <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	32 </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	33 </xml>
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 <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	35 <conditional name="output">
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	36 <param name="out_format" type="select" label="Output format">
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	37 <option value="6">Tabular (standard 12 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	38 <option value="ext" selected="True">Tabular (extended 25 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	39 <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	40 <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	41 <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	42 <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	43 <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	44 <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	45 <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	46 <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	47 <!--
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="-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	49 -->
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 </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	51 <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	52 <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	53 <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	54 <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	55 <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	56 <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	57 <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	58 <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	59 <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	60 <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	61 <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	62 <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	63 <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	64 <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	65 <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	66 <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	67 </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	68 <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	69 <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	70 <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	71 <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	72 <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	73 <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	74 <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	75 <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	76 <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	77 <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	78 <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	79 <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	80 <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	81 <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	82 </param>
15 c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	83 <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	84 <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	85 <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	86 <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	87 <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	88 <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	89 <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	90 <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	91 <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	92 <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	93 <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	94 </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	95 <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	96 <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	97 <!-- 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	98 <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	99 <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	100 <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	101 <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	102 </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	103 <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	104 <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	105 <!-- 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	106 <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	107 <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	108 <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	109 <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	110 </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	111 </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	112 <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	113 <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	114 <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	115 <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	116 <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	117 <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	118 <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	119 </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	120 </xml>
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	121 <xml name="input_scoring_matrix">
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	122 <param name="matrix" type="select" label="Scoring matrix">
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 <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	124 <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	125 <option value="BLOSUM62" selected="true">BLOSUM62 (default)</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	126 <option value="BLOSUM50">BLOSUM50</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	127 <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	128 <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	129 <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	130 <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	131 </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	132 </xml>
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	133 <xml name="input_query_gencode">
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	134 <param name="query_gencode" type="select" label="Query genetic code">
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	135 <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->
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	136 <option value="1" select="True">1. Standard</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	137 <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	138 <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	139 <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	140 <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	141 <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	142 <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	143 <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	144 <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	145 <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	146 <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	147 <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	148 <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	149 <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	150 <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	151 <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	152 <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	153 <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	154 </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	155 </xml>
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	156 <xml name="input_db_gencode">
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	157 <param name="db_gencode" type="select" label="Database/subject genetic code">
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	158 <!-- See http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi for details -->
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	159 <option value="1" select="True">1. Standard</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	160 <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	161 <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	162 <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	163 <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	164 <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	165 <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	166 <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	167 <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	168 <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	169 <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	170 <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	171 <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	172 <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	173 <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	174 <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	175 <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	176 <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	177 </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	178 </xml>
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	179 <xml name="input_conditional_nucleotide_db">
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	180 <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	181 <param name="db_opts_selector" type="select" label="Subject database/sequences">
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	182 <option value="db" selected="True">Locally installed BLAST database</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	183 <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	184 <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	185 </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	186 <when value="db">
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	187 <param name="database" type="select" label="Nucleotide BLAST database">
15 c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	188 <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	189 </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	190 <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	191 <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	192 </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	193 <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	194 <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	195 <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	196 <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	197 </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	198 <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	199 <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	200 <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	201 <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as 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	202 </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	203 </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	204 </xml>
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	205 <xml name="input_conditional_protein_db">
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	206 <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	207 <param name="db_opts_selector" type="select" label="Subject database/sequences">
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	208 <option value="db" selected="True">Locally installed BLAST database</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	209 <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	210 <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	211 </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	212 <when value="db">
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	213 <param name="database" type="select" 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	214 <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	215 </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	216 <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	217 <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	218 </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	219 <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	220 <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	221 <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	222 <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	223 </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	224 <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	225 <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	226 <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	227 <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as 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	228 </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	229 </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	230 </xml>
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	231 <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	232 <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	233 <param name="db_opts_selector" type="select" label="Protein domain database (PSSM)">
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	234 <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	235 <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	236 </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	237 <when value="db">
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	238 <param name="database" 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	239 <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	240 </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	241 <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	242 <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	243 </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	244 <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	245 <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	246 <param name="histdb" type="data" format="blastdbd" label="Protein domain 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	247 <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	248 </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	249 </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	250 </xml>
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	251 <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	252 <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	253 <param name="db_type" type="select" label="Type of 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	254 <option value="nucl" selected="True">Nucleotide</option>
4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	255 <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	256 </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	257 <when value="nucl">
4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	258 <param name="database" type="select" label="Nucleotide BLAST database">
15 c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	259 <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	260 </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	261 </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	262 <when value="prot">
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	263 <param name="database" type="select" 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	264 <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	265 </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	266 </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	267 </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	268 </xml>
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	269 <xml name="input_parse_deflines">
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	270 <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/>
4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	271 </xml>
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	272 <xml name="input_filter_query_default_false">
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	273 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" />
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	274 </xml>
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	275 <xml name="input_filter_query_default_true">
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	276 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />
4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	277 </xml>
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	278 <xml name="input_max_hits">
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	279 <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">
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	280 <validator type="in_range" min="0" />
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	281 </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	282 </xml>
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	283 <xml name="input_evalue">
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	284 <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
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	285 </xml>
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_word_size">
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	287 <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2.">
4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	288 <validator type="in_range" min="0" />
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 </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	290 </xml>
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	291 <xml name="input_strand">
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 <param name="strand" type="select" label="Query strand(s) to search against database/subject">
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="-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	294 <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	295 <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	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>
15 c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	298 <xml name="input_qcov_hsp_perc">
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	299 <param name="qcov_hsp_perc" type="float" value="0" min="0" max="100" label="Minimum query coverage per hsp (percentage, 0 to 100)" help="See also the output column qhspcov"/>
11 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	300 </xml>
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	301 <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	302 <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	303 <param name="adv_opts_selector" type="select" label="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	304 <option value="basic" selected="True">Hide Advanced Options</option>
4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	305 <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	306 </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	307 <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	308 <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	309 <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	310 </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	311 </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	312 </xml>
14 2fe07f50a41e Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations. peterjc parents: 13 diff changeset	313 <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	314 <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	315 <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	316 label="Restrict search of database to a given set of ID's"
2fe07f50a41e Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations. peterjc parents: 13 diff changeset	317 help="This feature provides a means to exclude ID's from a BLAST database search. The expectation values in the BLAST results are based upon the sequences actually searched, and not on the underlying database. Note this cannot be used when comparing against a FASTA file.">
2fe07f50a41e Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations. peterjc parents: 13 diff changeset	318 <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	319 <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	320 <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	321 <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	322 </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	323 <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	324 <when value="gilist">
2fe07f50a41e Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations. peterjc parents: 13 diff changeset	325 <param name="gilist" type="data" format="txt" label="Restrict search of database to GI's listed in this file"
2fe07f50a41e Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations. peterjc parents: 13 diff changeset	326 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	327 </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	328 <when value="negative_gilist">
2fe07f50a41e Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations. peterjc parents: 13 diff changeset	329 <param name="negative_gilist" type="data" format="txt" label="Restrict search of database to everything except the GI's listed in this file"
2fe07f50a41e Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations. peterjc parents: 13 diff changeset	330 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	331 </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	332 <when value="seqidlist">
2fe07f50a41e Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations. peterjc parents: 13 diff changeset	333 <param name="seqidlist" type="data" format="txt" label=" Restrict search of database to list of SeqId's"
2fe07f50a41e Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations. peterjc parents: 13 diff changeset	334 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	335 </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	336 </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	337 </xml>
15 c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	338 <token name="@ADV_QCOV_HSP_PERC@">
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	339 #if float(str($adv_opts.qcov_hsp_perc)) > 0:
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	340 -qcov_hsp_perc $adv_opts.qcov_hsp_perc
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	341 #end if
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	342 </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	343 <token name="@ADV_ID_LIST_FILTER@">
2fe07f50a41e Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations. peterjc parents: 13 diff changeset	344 #if $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'negative_gilist':
2fe07f50a41e Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations. peterjc parents: 13 diff changeset	345 -negative_gilist $adv_opts.adv_optional_id_files_opts.negative_gilist
2fe07f50a41e Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations. peterjc parents: 13 diff changeset	346 #elif $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'gilist':
2fe07f50a41e Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations. peterjc parents: 13 diff changeset	347 -gilist $adv_opts.adv_optional_id_files_opts.gilist
2fe07f50a41e Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations. peterjc parents: 13 diff changeset	348 #elif $adv_opts.adv_optional_id_files_opts.adv_optional_id_files_opts_selector == 'seqidlist':
2fe07f50a41e Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations. peterjc parents: 13 diff changeset	349 -seqidlist $adv_opts.adv_optional_id_files_opts.seqidlist
2fe07f50a41e Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations. peterjc parents: 13 diff changeset	350 #end if
2fe07f50a41e Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations. peterjc parents: 13 diff changeset	351 </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	352 <token name="@THREADS@">-num_threads "\${GALAXY_SLOTS:-8}"</token>
4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	353 <token name="@BLAST_DB_SUBJECT@">
4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	354 #if $db_opts.db_opts_selector == "db":
4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	355 -db "${db_opts.database.fields.path}"
4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	356 #elif $db_opts.db_opts_selector == "histdb":
16 b5f1f599d1fb Uploaded v0.1.04, fix regression with BLAST database from history peterjc parents: 15 diff changeset	357 -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}"
11 4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	358 #else:
4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	359 -subject "$db_opts.subject"
4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	360 #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	361 </token>
4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	362 <token name="@BLAST_OUTPUT@">-out "$output1"
4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	363 ##Set the extended list here so when we add things, saved workflows are not affected
13 623f727cdff1 Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields. peterjc parents: 11 diff changeset	364 #if str($output.out_format)=="ext":
11 4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	365 -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	366 #elif str($output.out_format)=="cols"
623f727cdff1 Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields. peterjc parents: 11 diff changeset	367 ##Pick your own columns. Galaxy gives us it comma separated, BLAST+ wants space separated:
623f727cdff1 Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields. peterjc parents: 11 diff changeset	368 ##TODO - Can we catch the user picking no columns and raise an error here?
623f727cdff1 Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields. peterjc parents: 11 diff changeset	369 #set cols = (str($output.std_cols)+","+str($output.ext_cols)+","+str($output.ids_cols)+","+str($output.misc_cols)+","+str($output.tax_cols)).replace("None", "").replace(",,", ",").replace(",", " ").strip()
623f727cdff1 Uploaded v0.1.00, uses BLAST+ 2.2.29, allows custom column selection for tabular output - including taxonomy fields. peterjc parents: 11 diff changeset	370 -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	371 #else:
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	372 -outfmt $output.out_format
11 4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	373 #end if
4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	374 </token>
15 c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	375 <token name="@ADV_FILTER_QUERY@">$adv_opts.filter_query</token>
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	376 <token name="@ADV_MAX_HITS@">
11 4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	377 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
15 c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	378 ## Note -max_target_seqs used to simply override -num_descriptions and -num_alignments
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	379 ## but this was changed in BLAST+ 2.2.27 onwards to force their use (raised with NCBI)
11 4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	380 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
15 c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	381 #if str($output.out_format) in ["6", "ext", "cols", "5"]:
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	382 ## Most output formats use this, including tabular and XML:
11 4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	383 -max_target_seqs $adv_opts.max_hits
15 c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	384 #else
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	385 ## Text and HTML output formats 0-4 currently need this instead:
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	386 -num_descriptions $adv_opts.max_hits -num_alignments $adv_opts.max_hits
11 4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	387 #end if
15 c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	388 #end if
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	389 </token>
c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	390 <token name="@ADV_WORD_SIZE@">
11 4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	391 #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
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 -word_size $adv_opts.word_size
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 #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	394 $adv_opts.parse_deflines
4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	395 </token>
4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	396 <!-- @ON_DB_SUBJECT@ is for use with @BLAST_DB_SUBJECT@ -->
4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	397 <token name="@ON_DB_SUBJECT@">#if str($db_opts.db_opts_selector)=='db'
4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	398 ${db_opts.database}
4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	399 #elif str($db_opts.db_opts_selector)=='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	400 ${db_opts.histdb.name}
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 #else
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	402 ${db_opts.subject.name}
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 #end if</token>
4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	404 <token name="@REFERENCES@">
15 c16c30e9ad5b Uploaded v0.1.03 (internal changes); v0.1.02 (BLAST+ 2.2.30 etc) peterjc parents: 14 diff changeset	405 Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson, Nicola Soranzo (2015).
17 697f40151eaf v0.1.05 - Update citation information now GigaScience paper is out peterjc parents: 16 diff changeset	406 NCBI BLAST+ integrated into Galaxy. GigaScience 4:39
697f40151eaf v0.1.05 - Update citation information now GigaScience paper is out peterjc parents: 16 diff changeset	407 http://dx.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	408
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 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	410 BLAST+: architecture and applications.
17 697f40151eaf v0.1.05 - Update citation information now GigaScience paper is out peterjc parents: 16 diff changeset	411 BMC Bioinformatics 15;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	412 http://dx.doi.org/10.1186/1471-2105-10-421
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
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 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	415 Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus
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 </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	417 <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	418 <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	419 <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	420 <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	421 </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	422 </xml>
11 4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	423 <token name="@OUTPUT_FORMAT@">Output 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	424
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 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	426 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	427
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 ====== ========= ============================================
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 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	430 ------ --------- --------------------------------------------
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	431 1 qseqid Query Seq-id (ID of your 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	432 2 sseqid Subject Seq-id (ID of the 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	433 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	434 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	435 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	436 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	437 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	438 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	439 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	440 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	441 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	442 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	443 ====== ========= ============================================
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	444
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	445 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	446 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	447 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	448 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	449 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	450 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	451
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	452 ====== ============= ===========================================
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	453 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	454 ------ ------------- -------------------------------------------
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	455 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	456 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	457 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	458 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	459 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	460 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	461 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	462 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	463 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	464 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	465 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	466 24 slen Subject sequence length
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	467 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	468 ====== ============= ===========================================
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
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	470 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	471 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	472 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	473
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	474 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	475 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	476
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 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	478 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	479 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	480 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	481 and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
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	482 </token>
4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	483 <token name="@FASTA_WARNING@">.. class:: warningmark
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
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	485 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	486 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	487 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	488 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	489 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	490 database first using makeblastdb and search against that.
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	491 </token>
4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	492 <token name="@SEARCH_TIME_WARNING@">.. class:: warningmark
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	493
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 Note. Database searches may take a substantial amount of time.
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	495 For large input datasets it is advisable to allow overnight processing.
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
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	497 -----
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 </token>
4c4a0da938ff Uploaded v0.0.22, now wraps BLAST+ 2.2.28 allowing extended tabular output to include the hit descriptions as column 25. peterjc parents: diff changeset	499 </macros>

Mercurial > repos > devteam > ncbi_blast_plus

annotate tools/ncbi_blast_plus/ncbi_macros.xml @ 19:7f3c448e119b draft