Mercurial > repos > bgruening > diamond

comparison diamond_view.xml @ 8:54f751e413f4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 75abf7d4b23ed7ae8abce80609d81b20bc882863"
author iuc
date Mon, 22 Mar 2021 13:21:23 +0000
parents 62c9df8382c2
children f921014aba5a
comparison
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7:62c9df8382c2 8:54f751e413f4
1 <tool id="bg_diamond_view" name="Diamond" version="@VERSION@" profile="19.01"> 1 <tool id="bg_diamond_view" name="Diamond view" version="@VERSION@" 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" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <expand macro="version_command" /> 8 <expand macro="version_command" />
9 <command><![CDATA[ 9 <command detect_errors="aggressive"><![CDATA[
10 ## need to link because diamont tries to open dataset_xxx.dat.daa 10 ## need to link because diamont tries to open dataset_xxx.dat.daa
11 ln -s '$daa' input.daa && 11 ln -s '$daa' input.daa &&
12 diamond 12 diamond
13 view 13 view
14 --threads \${GALAXY_SLOTS:-1}
14 --daa input.daa 15 --daa input.daa
15 @OUTPUT_ARGS@ 16 @OUTPUT_ARGS@
16 @HITFILTER_ARGS@ 17 @HITFILTER_ARGS@
17 $forwardonly 18 $forwardonly
18 --compress '0' 19 --compress '0'
41 </test> 42 </test>
42 <test> 43 <test>
43 <param name="daa" ftype="daa" value="diamond_results.daa" /> 44 <param name="daa" ftype="daa" value="diamond_results.daa" />
44 <conditional name="output"> 45 <conditional name="output">
45 <param name="outfmt" value="6"/> 46 <param name="outfmt" value="6"/>
46 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/> 47 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,cigar,scovhsp"/>
47 </conditional> 48 </conditional>
48 <output name="blast_tabular" file="diamond_results.tabular"/> 49 <output name="blast_tabular" file="diamond_view_results.tabular"/>
49 </test> 50 </test>
50 <test> 51 <test>
51 <param name="daa" ftype="daa" value="diamond_results.daa" /> 52 <param name="daa" ftype="daa" value="diamond_results.daa" />
52 <conditional name="output"> 53 <conditional name="output">
53 <param name="outfmt" value="101"/> 54 <param name="outfmt" value="101"/>