Mercurial > repos > yating-l > blastxmltopsl

comparison blastXmlToPsl.xml @ 0:ed804cd92001 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit cdddf587d82288414cfffd0ce6e312b4bf45a842-dirty
author yating-l
date Tue, 02 May 2017 13:21:49 -0400
parents
children 30f2068e8738
comparison
equal deleted inserted replaced
-1:000000000000 0:ed804cd92001
1 <tool id="blastXmlToPsl" name="blastXmlToPsl" version="0.1.0">
2 <requirements>
3 </requirements>
4 <stdio>
5 <exit_code range="1:" />
6 </stdio>
7 <command><![CDATA[
8 $__tool_directory__/blastXmlToPsl -convertToNucCoords $input $output
9 ]]></command>
10 <inputs>
11 <param type="data" name="input" format="xml" />
12 </inputs>
13 <outputs>
14 <data format="psl" name="output" />
15 </outputs>
16 <help><![CDATA[
17 blastXmlToPsl - convert blast XML output to PSLs
18
19 usage:
20 blastXmlToPsl [options] blastXml psl
21
22 options:
23 -scores=file - Write score information to this file. Format is:
24 strands qName qStart qEnd tName tStart tEnd bitscore eVal qDef tDef
25
26 -verbose=n - n >= 3 prints each line of file after parsing.
27 n >= 4 dumps the result of each query
28
29 -eVal=n n is e-value threshold to filter results. Format can be either
30 an integer, double or 1e-10. Default is no filter.
31
32 -pslx - create PSLX output (includes sequences for blocks)
33
34 -convertToNucCoords - convert protein to nucleic alignments to nucleic
35 to nucleic coordinates
36
37 -qName=src - define element used to obtain the qName. The following
38 values are support:
39 - query-ID - use contents of the <Iteration_query-ID> element if it
40 exists, otherwise use <BlastOutput_query-ID>
41 - query-def0 - use the first white-space separated word of the
42 <Iteration_query-def> element if it exists, otherwise the first word
43 of <BlastOutput_query-def>.
44
45 Default is query-def0.
46
47 -tName=src - define element used to obtain the tName. The following
48 values are support:
49 - Hit_id - use contents of the <Hit-id> element.
50 - Hit_def0 - use the first white-space separated word of the
51 <Hit_def> element.
52 - Hit_accession - contents of the <Hit_accession> element.
53
54 Default is Hit-def0.
55
56 -forcePsiBlast - treat as output of PSI-BLAST. blast-2.2.16 and maybe
57 others indentify psiblast as blastp.
58
59 Output only results of last round from PSI BLAST
60 ]]></help>
61 </tool>