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comparison diamond_view.xml @ 6:64be1ac21109 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
author bgruening
date Thu, 27 Sep 2018 06:30:30 -0400
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children 62c9df8382c2
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5:3c6b132b154a 6:64be1ac21109
1 <tool id="bg_diamond_view" name="Diamond" version="@VERSION@">
2 <description>generate formatted output from DAA files</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <expand macro="version_command" />
9 <command><![CDATA[
10 ## need to link because diamont tries to open dataset_xxx.dat.daa
11 ln -s '$daa' input.daa &&
12 diamond
13 view
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 <expand macro="output_type_macro" />
24 <expand macro="hit_filter_macro" />
25 <param argument="--forwardonly" type="boolean" truevalue="--forwardonly" falsevalue="" checked="false" label="only show alignments of forward strand" help=""/>
26 </inputs>
27 <outputs>
28 <expand macro="output_macro" />
29 </outputs>
30 <tests>
31 <test>
32 <param name="daa" ftype="daa" value="diamond_results.daa" />
33 <conditional name="output">
34 <param name="outfmt" value="5"/>
35 </conditional>
36 <conditional name="hit_filter">
37 <param name="hit_filter_select" value="max"/>
38 <param name="max_target_seqs" value="1" />
39 </conditional>
40 <output name="blast_tabular" file="diamond_results.xml"/>
41 </test>
42 <test>
43 <param name="daa" ftype="daa" value="diamond_results.daa" />
44 <conditional name="output">
45 <param name="outfmt" value="6"/>
46 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
47 </conditional>
48 <output name="blast_tabular" file="diamond_results.tabular"/>
49 </test>
50 <test>
51 <param name="daa" ftype="daa" value="diamond_results.daa" />
52 <conditional name="output">
53 <param name="outfmt" value="101"/>
54 </conditional>
55 <conditional name="hit_filter">
56 <param name="hit_filter_select" value="top"/>
57 <param name="max_target_seqs" value="1" />
58 </conditional>
59 <param name="forwardonly" value="--forwardonly" />
60 <output name="blast_tabular" file="diamond_results.sam"/>
61 </test>
62 </tests>
63
64 <help>
65 <![CDATA[
66
67 **What it does**
68
69 Converts diamond daa files to multiple other formats.
70
71 **Input**
72
73 Input data is a daa file.
74
75
76 **Output**
77
78 Alignment results in BLAST format (pairwise/tabular), xml, sam, taxonomic (Note the latter does not work with the current diamond version. )
79
80 BLAST tables contain the following columns.
81
82 Column Description
83 1 Query Seq-id (ID of your sequence)
84 2 Subject Seq-id (ID of the database hit)
85 3 Percentage of identical matches
86 4 Alignment length
87 5 Number of mismatches
88 6 Number of gap openings
89 7 Start of alignment in query
90 8 End of alignment in query
91 9 Start of alignment in subject (database hit)
92 10 End of alignment in subject (database hit)
93 11 Expectation value (E-value)
94 12 Bit score
95 ]]>
96 </help>
97 <expand macro="citations" />
98 </tool>