Mercurial > repos > bgruening > diamond

comparison diamond_view.xml @ 10:1e3323a44643 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"
author iuc
date Fri, 22 Apr 2022 13:51:34 +0000
parents f921014aba5a
children
comparison
equal deleted inserted replaced
9:f921014aba5a 10:1e3323a44643
1 <tool id="bg_diamond_view" name="Diamond view" version="@TOOL_VERSION@.1" profile="19.01"> 1 <tool id="bg_diamond_view" name="Diamond view" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01">
2 <description>generate formatted output from DAA files</description> 2 <description>generate formatted output from DAA files</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
19 --compress '0' 19 --compress '0'
20 ]]> 20 ]]>
21 </command> 21 </command>
22 <inputs> 22 <inputs>
23 <param argument="--daa" type="data" format="daa" label="input file in DAA format" /> 23 <param argument="--daa" type="data" format="daa" label="input file in DAA format" />
24 <expand macro="output_type_macro" /> 24 <section name="output_section" title="Output options">
25 <expand macro="output_type_macro" />
26 </section>
25 <expand macro="hit_filter_macro" /> 27 <expand macro="hit_filter_macro" />
26 <param argument="--forwardonly" type="boolean" truevalue="--forwardonly" falsevalue="" checked="false" label="only show alignments of forward strand" help=""/> 28 <param argument="--forwardonly" type="boolean" truevalue="--forwardonly" falsevalue="" checked="false" label="only show alignments of forward strand" help=""/>
27 </inputs> 29 </inputs>
28 <outputs> 30 <outputs>
29 <expand macro="output_macro" /> 31 <expand macro="output_macro" />
30 </outputs> 32 </outputs>
31 <tests> 33 <tests>
32 <test expect_num_outputs="1"> 34 <test expect_num_outputs="1">
33 <param name="daa" ftype="daa" value="diamond_results.daa" /> 35 <param name="daa" ftype="daa" value="diamond_results.daa" />
34 <conditional name="output"> 36 <section name="output_section">
35 <param name="outfmt" value="5"/> 37 <conditional name="output">
36 </conditional> 38 <param name="outfmt" value="5"/>
39 </conditional>
40 </section>
37 <conditional name="hit_filter"> 41 <conditional name="hit_filter">
38 <param name="hit_filter_select" value="max"/> 42 <param name="hit_filter_select" value="max"/>
39 <param name="max_target_seqs" value="1" /> 43 <param name="max_target_seqs" value="1" />
40 </conditional> 44 </conditional>
41 <output name="blast_tabular" file="diamond_results.xml"/> 45 <output name="blast_tabular" file="diamond_results.xml"/>
42 </test> 46 </test>
43 <test expect_num_outputs="1"> 47 <test expect_num_outputs="1">
44 <param name="daa" ftype="daa" value="diamond_results.daa" /> 48 <param name="daa" ftype="daa" value="diamond_results.daa" />
45 <conditional name="output"> 49 <section name="output_section">
46 <param name="outfmt" value="6"/> 50 <conditional name="output">
47 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,cigar,scovhsp"/> 51 <param name="outfmt" value="6"/>
48 </conditional> 52 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,cigar,scovhsp"/>
53 </conditional>
54 </section>
49 <output name="blast_tabular" file="diamond_view_results.tabular"/> 55 <output name="blast_tabular" file="diamond_view_results.tabular"/>
50 </test> 56 </test>
51 <test expect_num_outputs="1"> 57 <test expect_num_outputs="1">
52 <param name="daa" ftype="daa" value="diamond_results.daa" /> 58 <param name="daa" ftype="daa" value="diamond_results.daa" />
53 <conditional name="output"> 59 <section name="output_section">
54 <param name="outfmt" value="101"/> 60 <conditional name="output">
55 </conditional> 61 <param name="outfmt" value="101"/>
62 </conditional>
63 </section>
56 <conditional name="hit_filter"> 64 <conditional name="hit_filter">
57 <param name="hit_filter_select" value="top"/> 65 <param name="hit_filter_select" value="top"/>
58 <param name="max_target_seqs" value="1" /> 66 <param name="max_target_seqs" value="1" />
59 </conditional> 67 </conditional>
60 <param name="forwardonly" value="--forwardonly" /> 68 <param name="forwardonly" value="--forwardonly" />