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comparison chimera.xml @ 2:f29e21388219 draft

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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
comparison
equal deleted inserted replaced
1:8c4e2933a17a 2:f29e21388219
1 <tool id="vsearch_chimera_detection" name="VSearch chimera detection" version="@VERSION@.0"> 1 <tool id="vsearch_chimera_detection" name="VSearch chimera detection" version="@VERSION@.1">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>vsearch_macros.xml</import> 4 <import>vsearch_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
8 <expand macro="version_command" /> 8 <expand macro="version_command" />
9 <command> 9 <command>
10 <![CDATA[ 10 <![CDATA[
11 vsearch 11 vsearch
12 @GENERAL@ 12 @GENERAL@
13 --abskew $abskew 13 --abskew "${abskew}"
14 --chimeras $outfile 14 --chimeras "${outfile}"
15 --dn $dn 15 --dn "${dn}"
16 --mindiffs $mindiffs 16 --mindiffs "${mindiffs}"
17 --mindiv $mindiv 17 --mindiv "${mindiv}"
18 --minh $minh 18 --minh "${minh}"
19 --xn $xn 19 --xn "${xn}"
20 $self_param 20 $self_param
21 $selfid_param 21 $selfid_param
22 #if $detection_mode.detection_mode_select == 'denovo': 22 #if $detection_mode.detection_mode_select == 'denovo':
23 --uchime_denovo $detection_mode.infile_denovo 23 --uchime_denovo "${detection_mode.infile_denovo}"
24 #else: 24 #else:
25 --uchime_ref $detection_mode.infile_reference 25 --uchime_ref $detection_mode.infile_reference
26 --db $detection_mode.db 26 --db "${detection_mode.db}"
27 #end if 27 #end if
28 28
29 #if 'nonchimeras' in str($outputs): 29 #if 'nonchimeras' in str($outputs).split( "," ):
30 --nonchimeras $nonchimeras 30 --nonchimeras "${nonchimeras}"
31 #end if 31 #end if
32 #if 'uchimealns' in str($outputs): 32 #if 'uchimealns' in str($outputs).split( "," ):
33 --uchimealns $uchimealns 33 --uchimealns "${uchimealns}"
34 #end if 34 #end if
35 #if 'uchimeout' in str($outputs): 35 #if 'uchimeout' in str($outputs).split( "," ):
36 --uchimeout $uchimeout 36 --uchimeout "${uchimeout}"
37 #end if 37 #end if
38 38
39 ]]> 39 ]]>
40 </command> 40 </command>
41 <inputs> 41 <inputs>
77 77
78 </inputs> 78 </inputs>
79 <outputs> 79 <outputs>
80 <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" /> 80 <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" />
81 <data name="nonchimeras" format="fasta" label="${tool.name} on ${on_string}: Non Chimera"> 81 <data name="nonchimeras" format="fasta" label="${tool.name} on ${on_string}: Non Chimera">
82 <filter>'nonchimeras' in outputs</filter> 82 <filter>outputs and 'nonchimeras' in outputs</filter>
83 </data> 83 </data>
84 <data name="uchimealns" format="fasta" label="${tool.name} on ${on_string}: Chimera Alignments"> 84 <data name="uchimealns" format="fasta" label="${tool.name} on ${on_string}: Chimera Alignments">
85 <filter>'uchimealns' in outputs</filter> 85 <filter>outputs and 'uchimealns' in outputs</filter>
86 </data> 86 </data>
87 <data name="uchimeout" format="tabular" label="${tool.name} on ${on_string}: Chimera Information"> 87 <data name="uchimeout" format="tabular" label="${tool.name} on ${on_string}: Chimera Information">
88 <filter>'uchimeout' in outputs</filter> 88 <filter>outputs and 'uchimeout' in outputs</filter>
89 </data> 89 </data>
90 </outputs> 90 </outputs>
91 <tests> 91 <tests>
92 <test> 92 <test>
93 <param name="detection_mode_select" value="denovo"/> 93 <param name="detection_mode_select" value="denovo"/>
122 --uchimeout5 make output compatible with uchime version 5 122 --uchimeout5 make output compatible with uchime version 5
123 --xn REAL 'no' vote weight (8.0) 123 --xn REAL 'no' vote weight (8.0)
124 124
125 @EXTERNAL_DOCUMENTATION@ 125 @EXTERNAL_DOCUMENTATION@
126 126
127 -------
128
129 @REFERENCES@
130
131 127
132 ]]> 128 ]]>
133 </help> 129 </help>
134 <expand macro="citations" /> 130 <expand macro="citations" />
135 </tool> 131 </tool>