Mercurial > repos > iuc > vsearch
comparison chimera.xml @ 2:f29e21388219 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch commit 64c1c4c664c6a131d897f574dc849f5668fa97d2
author | iuc |
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date | Thu, 17 Dec 2015 12:53:39 -0500 |
parents | fae6527990af |
children | 4258854759ba |
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1:8c4e2933a17a | 2:f29e21388219 |
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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> |