Mercurial > repos > bgruening > diamond
diff diamond_view.xml @ 8:54f751e413f4 draft
"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 |
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--- a/diamond_view.xml Tue Dec 03 17:40:05 2019 -0500 +++ b/diamond_view.xml Mon Mar 22 13:21:23 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="bg_diamond_view" name="Diamond" version="@VERSION@" profile="19.01"> +<tool id="bg_diamond_view" name="Diamond view" version="@VERSION@" profile="19.01"> <description>generate formatted output from DAA files</description> <macros> <import>macros.xml</import> @@ -6,11 +6,12 @@ <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> - <command><![CDATA[ + <command detect_errors="aggressive"><![CDATA[ ## need to link because diamont tries to open dataset_xxx.dat.daa ln -s '$daa' input.daa && diamond view + --threads \${GALAXY_SLOTS:-1} --daa input.daa @OUTPUT_ARGS@ @HITFILTER_ARGS@ @@ -43,9 +44,9 @@ <param name="daa" ftype="daa" value="diamond_results.daa" /> <conditional name="output"> <param name="outfmt" value="6"/> - <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/> + <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,cigar,scovhsp"/> </conditional> - <output name="blast_tabular" file="diamond_results.tabular"/> + <output name="blast_tabular" file="diamond_view_results.tabular"/> </test> <test> <param name="daa" ftype="daa" value="diamond_results.daa" />