Mercurial > repos > bgruening > diamond

comparison diamond_view.xml @ 7:62c9df8382c2 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
author bgruening
date Tue, 03 Dec 2019 17:40:05 -0500
parents 64be1ac21109
children 54f751e413f4
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6:64be1ac21109 7:62c9df8382c2
1 <tool id="bg_diamond_view" name="Diamond" version="@VERSION@"> 1 <tool id="bg_diamond_view" name="Diamond" 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><![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 --daa input.daa 14 --daa input.daa
15 @OUTPUT_ARGS@ 15 @OUTPUT_ARGS@
55 <conditional name="hit_filter"> 55 <conditional name="hit_filter">
56 <param name="hit_filter_select" value="top"/> 56 <param name="hit_filter_select" value="top"/>
57 <param name="max_target_seqs" value="1" /> 57 <param name="max_target_seqs" value="1" />
58 </conditional> 58 </conditional>
59 <param name="forwardonly" value="--forwardonly" /> 59 <param name="forwardonly" value="--forwardonly" />
60 <output name="blast_tabular" file="diamond_results.sam"/> 60 <output name="blast_tabular" file="diamond_results.sam" lines_diff="2"/>
61 </test> 61 </test>
62 </tests> 62 </tests>
63 63
64 <help> 64 <help>
65 <![CDATA[ 65 <![CDATA[