Mercurial > repos > iuc > vsearch
diff chimera.xml @ 2:f29e21388219 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
author | iuc |
---|---|
date | Thu, 17 Dec 2015 12:53:39 -0500 |
parents | fae6527990af |
children | 4258854759ba |
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--- a/chimera.xml Wed Aug 26 13:34:22 2015 -0400 +++ b/chimera.xml Thu Dec 17 12:53:39 2015 -0500 @@ -1,4 +1,4 @@ -<tool id="vsearch_chimera_detection" name="VSearch chimera detection" version="@VERSION@.0"> +<tool id="vsearch_chimera_detection" name="VSearch chimera detection" version="@VERSION@.1"> <description></description> <macros> <import>vsearch_macros.xml</import> @@ -10,30 +10,30 @@ <![CDATA[ vsearch @GENERAL@ - --abskew $abskew - --chimeras $outfile - --dn $dn - --mindiffs $mindiffs - --mindiv $mindiv - --minh $minh - --xn $xn + --abskew "${abskew}" + --chimeras "${outfile}" + --dn "${dn}" + --mindiffs "${mindiffs}" + --mindiv "${mindiv}" + --minh "${minh}" + --xn "${xn}" $self_param $selfid_param #if $detection_mode.detection_mode_select == 'denovo': - --uchime_denovo $detection_mode.infile_denovo + --uchime_denovo "${detection_mode.infile_denovo}" #else: --uchime_ref $detection_mode.infile_reference - --db $detection_mode.db + --db "${detection_mode.db}" #end if - #if 'nonchimeras' in str($outputs): - --nonchimeras $nonchimeras + #if 'nonchimeras' in str($outputs).split( "," ): + --nonchimeras "${nonchimeras}" #end if - #if 'uchimealns' in str($outputs): - --uchimealns $uchimealns + #if 'uchimealns' in str($outputs).split( "," ): + --uchimealns "${uchimealns}" #end if - #if 'uchimeout' in str($outputs): - --uchimeout $uchimeout + #if 'uchimeout' in str($outputs).split( "," ): + --uchimeout "${uchimeout}" #end if ]]> @@ -79,13 +79,13 @@ <outputs> <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" /> <data name="nonchimeras" format="fasta" label="${tool.name} on ${on_string}: Non Chimera"> - <filter>'nonchimeras' in outputs</filter> + <filter>outputs and 'nonchimeras' in outputs</filter> </data> <data name="uchimealns" format="fasta" label="${tool.name} on ${on_string}: Chimera Alignments"> - <filter>'uchimealns' in outputs</filter> + <filter>outputs and 'uchimealns' in outputs</filter> </data> <data name="uchimeout" format="tabular" label="${tool.name} on ${on_string}: Chimera Information"> - <filter>'uchimeout' in outputs</filter> + <filter>outputs and 'uchimeout' in outputs</filter> </data> </outputs> <tests> @@ -124,10 +124,6 @@ @EXTERNAL_DOCUMENTATION@ -------- - -@REFERENCES@ - ]]> </help>