|
59
|
1 <tool id="pl_diamond_view" name="PL_Diamond view" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01">
|
|
|
2 <description>generate formatted output from DAA files</description>
|
|
|
3 <macros>
|
|
|
4 <import>macros.xml</import>
|
|
|
5 </macros>
|
|
|
6 <expand macro="stdio" />
|
|
|
7 <expand macro="version_command" />
|
|
|
8 <command detect_errors="aggressive"><![CDATA[
|
|
|
9 ## need to link because diamont tries to open dataset_xxx.dat.daa
|
|
|
10 ln -s '$daa' input.daa &&
|
|
|
11 /usr/bin/diamond
|
|
|
12 view
|
|
|
13 --threads \${GALAXY_SLOTS:-1}
|
|
|
14 --daa input.daa
|
|
|
15 @OUTPUT_ARGS@
|
|
|
16 @HITFILTER_ARGS@
|
|
|
17 $forwardonly
|
|
|
18 --compress '0'
|
|
|
19 ]]>
|
|
|
20 </command>
|
|
|
21 <inputs>
|
|
|
22 <param argument="--daa" type="data" format="daa" label="input file in DAA format" />
|
|
|
23 <section name="output_section" title="Output options">
|
|
|
24 <expand macro="output_type_macro" />
|
|
|
25 </section>
|
|
|
26 <expand macro="hit_filter_macro" />
|
|
|
27 <param argument="--forwardonly" type="boolean" truevalue="--forwardonly" falsevalue="" checked="false" label="only show alignments of forward strand" help=""/>
|
|
|
28 </inputs>
|
|
|
29 <outputs>
|
|
|
30 <expand macro="output_macro" />
|
|
|
31 </outputs>
|
|
|
32 <help>
|
|
|
33 <![CDATA[
|
|
|
34
|
|
|
35 **What it does**
|
|
|
36
|
|
|
37 Converts diamond daa files to multiple other formats.
|
|
|
38
|
|
|
39 **Input**
|
|
|
40
|
|
|
41 Input data is a daa file.
|
|
|
42
|
|
|
43
|
|
|
44 **Output**
|
|
|
45
|
|
|
46 Alignment results in BLAST format (pairwise/tabular), xml, sam, taxonomic (Note the latter does not work with the current diamond version. )
|
|
|
47
|
|
|
48 BLAST tables contain the following columns.
|
|
|
49
|
|
|
50 Column Description
|
|
|
51 1 Query Seq-id (ID of your sequence)
|
|
|
52 2 Subject Seq-id (ID of the database hit)
|
|
|
53 3 Percentage of identical matches
|
|
|
54 4 Alignment length
|
|
|
55 5 Number of mismatches
|
|
|
56 6 Number of gap openings
|
|
|
57 7 Start of alignment in query
|
|
|
58 8 End of alignment in query
|
|
|
59 9 Start of alignment in subject (database hit)
|
|
|
60 10 End of alignment in subject (database hit)
|
|
|
61 11 Expectation value (E-value)
|
|
|
62 12 Bit score
|
|
|
63 ]]>
|
|
|
64 </help>
|
|
|
65 <expand macro="citations" />
|
|
|
66 </tool>
|
